-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447011 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1451016
-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA11840.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 69166
-> Sites to keep[1] from pop1: 69166
-> [readdata] lastread:69166 posi:14000296
-> Comparing positions: 1 with 0 has:69166
-> Only read nSites: 69166 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 74338
-> Sites to keep[10] from pop1: 74338
-> [readdata] lastread:74338 posi:14000296
-> Comparing positions: 1 with 0 has:143504
-> Only read nSites: 143504 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 72548
-> Sites to keep[11] from pop1: 72548
-> [readdata] lastread:72548 posi:14000296
-> Comparing positions: 1 with 0 has:216052
-> Only read nSites: 216052 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 74841
-> Sites to keep[12] from pop1: 74841
-> [readdata] lastread:74841 posi:14000296
-> Comparing positions: 1 with 0 has:290893
-> Only read nSites: 290893 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 69510
-> Sites to keep[16] from pop1: 69510
-> [readdata] lastread:69510 posi:14000296
-> Comparing positions: 1 with 0 has:360403
-> Only read nSites: 360403 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 55424
-> Sites to keep[17] from pop1: 55424
-> [readdata] lastread:55424 posi:14000296
-> Comparing positions: 1 with 0 has:415827
-> Only read nSites: 415827 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 63016
-> Sites to keep[18] from pop1: 63016
-> [readdata] lastread:63016 posi:14000296
-> Comparing positions: 1 with 0 has:478843
-> Only read nSites: 478843 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 53675
-> Sites to keep[19] from pop1: 53675
-> [readdata] lastread:53675 posi:14000296
-> Comparing positions: 1 with 0 has:532518
-> Only read nSites: 532518 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 58633
-> Sites to keep[2] from pop1: 58633
-> [readdata] lastread:58633 posi:14000296
-> Comparing positions: 1 with 0 has:591151
-> Only read nSites: 591151 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 62256
-> Sites to keep[20] from pop1: 62256
-> [readdata] lastread:62256 posi:14000296
-> Comparing positions: 1 with 0 has:653407
-> Only read nSites: 653407 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 55750
-> Sites to keep[3] from pop1: 55750
-> [readdata] lastread:55750 posi:14000296
-> Comparing positions: 1 with 0 has:709157
-> Only read nSites: 709157 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 69568
-> Sites to keep[4] from pop1: 69568
-> [readdata] lastread:69568 posi:14000296
-> Comparing positions: 1 with 0 has:778725
-> Only read nSites: 778725 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 70002
-> Sites to keep[5] from pop1: 70002
-> [readdata] lastread:70002 posi:14000296
-> Comparing positions: 1 with 0 has:848727
-> Only read nSites: 848727 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 72579
-> Sites to keep[6] from pop1: 72579
-> [readdata] lastread:72579 posi:14000296
-> Comparing positions: 1 with 0 has:921306
-> Only read nSites: 921306 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 63710
-> Sites to keep[7] from pop1: 63710
-> [readdata] lastread:63710 posi:14000296
-> Comparing positions: 1 with 0 has:985016
-> Only read nSites: 985016 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 61147
-> Sites to keep[8] from pop1: 61147
-> [readdata] lastread:61147 posi:14000296
-> Comparing positions: 1 with 0 has:1046163
-> Only read nSites: 1046163 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 73554
-> Sites to keep[9] from pop1: 73554
-> [readdata] lastread:73554 posi:14000296
-> Comparing positions: 1 with 0 has:1119717
-> Only read nSites: 1119717 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1119717
------------
startlik=-2593701.166205
lik[2]=-198864.341967 diff=2.394837e+06 alpha:1.000000 sr2:4.120179e-01
lik[5]=-100104.713145 diff=9.875963e+04 alpha:1.351338 sr2:1.203756e-02
lik[8]=-100020.577949 diff=8.413520e+01 alpha:2.559383 sr2:2.584763e-08
lik[11]=-99988.041884 diff=3.253607e+01 alpha:2.956788 sr2:1.779950e-10
lik[14]=-99977.038663 diff=1.100322e+01 alpha:4.000000 sr2:3.556392e-10
lik[17]=-99976.837398 diff=2.012650e-01 alpha:3.368543 sr2:2.603086e-11
-> Breaking EM(sq2) at iter:19, sqrt(sq2):6.949050e-07
likelihood: -99976.837398
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447013 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1450698
-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA07357.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 72998
-> Sites to keep[1] from pop1: 72998
-> [readdata] lastread:72998 posi:14000253
-> Comparing positions: 1 with 0 has:72998
-> Only read nSites: 72998 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80472
-> Sites to keep[10] from pop1: 80472
-> [readdata] lastread:80472 posi:14000253
-> Comparing positions: 1 with 0 has:153470
-> Only read nSites: 153470 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 77499
-> Sites to keep[11] from pop1: 77499
-> [readdata] lastread:77499 posi:14000253
-> Comparing positions: 1 with 0 has:230969
-> Only read nSites: 230969 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 79830
-> Sites to keep[12] from pop1: 79830
-> [readdata] lastread:79830 posi:14000253
-> Comparing positions: 1 with 0 has:310799
-> Only read nSites: 310799 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 72768
-> Sites to keep[16] from pop1: 72768
-> [readdata] lastread:72768 posi:14000253
-> Comparing positions: 1 with 0 has:383567
-> Only read nSites: 383567 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 58417
-> Sites to keep[17] from pop1: 58417
-> [readdata] lastread:58417 posi:14000253
-> Comparing positions: 1 with 0 has:441984
-> Only read nSites: 441984 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 65098
-> Sites to keep[18] from pop1: 65098
-> [readdata] lastread:65098 posi:14000253
-> Comparing positions: 1 with 0 has:507082
-> Only read nSites: 507082 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 65927
-> Sites to keep[19] from pop1: 65927
-> [readdata] lastread:65927 posi:14000253
-> Comparing positions: 1 with 0 has:573009
-> Only read nSites: 573009 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 60813
-> Sites to keep[2] from pop1: 60813
-> [readdata] lastread:60813 posi:14000253
-> Comparing positions: 1 with 0 has:633822
-> Only read nSites: 633822 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 63185
-> Sites to keep[20] from pop1: 63185
-> [readdata] lastread:63185 posi:14000253
-> Comparing positions: 1 with 0 has:697007
-> Only read nSites: 697007 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 57388
-> Sites to keep[3] from pop1: 57388
-> [readdata] lastread:57388 posi:14000253
-> Comparing positions: 1 with 0 has:754395
-> Only read nSites: 754395 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 73769
-> Sites to keep[4] from pop1: 73769
-> [readdata] lastread:73769 posi:14000253
-> Comparing positions: 1 with 0 has:828164
-> Only read nSites: 828164 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 75862
-> Sites to keep[5] from pop1: 75862
-> [readdata] lastread:75862 posi:14000253
-> Comparing positions: 1 with 0 has:904026
-> Only read nSites: 904026 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 77910
-> Sites to keep[6] from pop1: 77910
-> [readdata] lastread:77910 posi:14000253
-> Comparing positions: 1 with 0 has:981936
-> Only read nSites: 981936 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 67142
-> Sites to keep[7] from pop1: 67142
-> [readdata] lastread:67142 posi:14000253
-> Comparing positions: 1 with 0 has:1049078
-> Only read nSites: 1049078 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 63912
-> Sites to keep[8] from pop1: 63912
-> [readdata] lastread:63912 posi:14000253
-> Comparing positions: 1 with 0 has:1112990
-> Only read nSites: 1112990 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 76930
-> Sites to keep[9] from pop1: 76930
-> [readdata] lastread:76930 posi:14000253
-> Comparing positions: 1 with 0 has:1189920
-> Only read nSites: 1189920 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1189920
------------
startlik=-3295499.379610
lik[2]=-671936.971750 diff=2.623562e+06 alpha:1.000000 sr2:3.079325e-01
lik[5]=-111757.000553 diff=5.601800e+05 alpha:1.705500 sr2:1.773156e-01
lik[8]=-111118.729808 diff=6.382707e+02 alpha:1.502014 sr2:3.776958e-07
lik[11]=-111104.701401 diff=1.402841e+01 alpha:2.753213 sr2:1.159374e-09
lik[14]=-111021.389502 diff=8.331190e+01 alpha:1.443829 sr2:6.760094e-12
lik[17]=-110840.982706 diff=1.804068e+02 alpha:2.558721 sr2:2.761461e-09
lik[20]=-110839.909743 diff=1.072963e+00 alpha:1.672894 sr2:1.402133e-10
lik[23]=-110839.871314 diff=3.842885e-02 alpha:4.000000 sr2:3.133923e-12
-> Breaking EM(sr2) at iter:24, sqrt(sr2):7.629226e-08
likelihood: -110839.871314
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447016 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1265795
-> The choice of -nSites will require atleast: 48.286247 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA11832.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 60083
-> Sites to keep[1] from pop1: 60083
-> [readdata] lastread:60083 posi:14000319
-> Comparing positions: 1 with 0 has:60083
-> Only read nSites: 60083 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 66691
-> Sites to keep[10] from pop1: 66691
-> [readdata] lastread:66691 posi:14000319
-> Comparing positions: 1 with 0 has:126774
-> Only read nSites: 126774 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 63721
-> Sites to keep[11] from pop1: 63721
-> [readdata] lastread:63721 posi:14000319
-> Comparing positions: 1 with 0 has:190495
-> Only read nSites: 190495 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 66430
-> Sites to keep[12] from pop1: 66430
-> [readdata] lastread:66430 posi:14000319
-> Comparing positions: 1 with 0 has:256925
-> Only read nSites: 256925 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 60907
-> Sites to keep[16] from pop1: 60907
-> [readdata] lastread:60907 posi:14000319
-> Comparing positions: 1 with 0 has:317832
-> Only read nSites: 317832 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 47428
-> Sites to keep[17] from pop1: 47428
-> [readdata] lastread:47428 posi:14000319
-> Comparing positions: 1 with 0 has:365260
-> Only read nSites: 365260 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 54225
-> Sites to keep[18] from pop1: 54225
-> [readdata] lastread:54225 posi:14000319
-> Comparing positions: 1 with 0 has:419485
-> Only read nSites: 419485 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 50453
-> Sites to keep[19] from pop1: 50453
-> [readdata] lastread:50453 posi:14000319
-> Comparing positions: 1 with 0 has:469938
-> Only read nSites: 469938 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 49280
-> Sites to keep[2] from pop1: 49280
-> [readdata] lastread:49280 posi:14000319
-> Comparing positions: 1 with 0 has:519218
-> Only read nSites: 519218 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 50084
-> Sites to keep[20] from pop1: 50084
-> [readdata] lastread:50084 posi:14000319
-> Comparing positions: 1 with 0 has:569302
-> Only read nSites: 569302 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 46955
-> Sites to keep[3] from pop1: 46955
-> [readdata] lastread:46955 posi:14000319
-> Comparing positions: 1 with 0 has:616257
-> Only read nSites: 616257 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 61716
-> Sites to keep[4] from pop1: 61716
-> [readdata] lastread:61716 posi:14000319
-> Comparing positions: 1 with 0 has:677973
-> Only read nSites: 677973 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 62941
-> Sites to keep[5] from pop1: 62941
-> [readdata] lastread:62941 posi:14000319
-> Comparing positions: 1 with 0 has:740914
-> Only read nSites: 740914 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 63995
-> Sites to keep[6] from pop1: 63995
-> [readdata] lastread:63995 posi:14000319
-> Comparing positions: 1 with 0 has:804909
-> Only read nSites: 804909 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 53747
-> Sites to keep[7] from pop1: 53747
-> [readdata] lastread:53747 posi:14000319
-> Comparing positions: 1 with 0 has:858656
-> Only read nSites: 858656 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 51888
-> Sites to keep[8] from pop1: 51888
-> [readdata] lastread:51888 posi:14000319
-> Comparing positions: 1 with 0 has:910544
-> Only read nSites: 910544 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 64862
-> Sites to keep[9] from pop1: 64862
-> [readdata] lastread:64862 posi:14000319
-> Comparing positions: 1 with 0 has:975406
-> Only read nSites: 975406 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 975406
------------
startlik=-1695470.779729
lik[2]=-135885.756887 diff=1.559585e+06 alpha:1.000000 sr2:4.720139e-01
lik[5]=-88454.733074 diff=4.743102e+04 alpha:1.425159 sr2:3.419794e-03
lik[8]=-88244.916470 diff=2.098166e+02 alpha:2.071332 sr2:1.958948e-07
lik[11]=-88195.404468 diff=4.951200e+01 alpha:4.000000 sr2:4.299315e-09
lik[14]=-88190.550578 diff=4.853891e+00 alpha:3.025225 sr2:2.676804e-10
lik[17]=-88189.965506 diff=5.850715e-01 alpha:3.957403 sr2:3.296353e-11
lik[20]=-88189.942356 diff=2.315016e-02 alpha:2.244944 sr2:4.461082e-12
-> Breaking EM(sr2) at iter:21, sqrt(sr2):4.918831e-07
likelihood: -88189.942356
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447017 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1372028
-> The choice of -nSites will require atleast: 52.338715 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA06994.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 69322
-> Sites to keep[1] from pop1: 69322
-> [readdata] lastread:69322 posi:14000242
-> Comparing positions: 1 with 0 has:69322
-> Only read nSites: 69322 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 75456
-> Sites to keep[10] from pop1: 75456
-> [readdata] lastread:75456 posi:14000242
-> Comparing positions: 1 with 0 has:144778
-> Only read nSites: 144778 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 74980
-> Sites to keep[11] from pop1: 74980
-> [readdata] lastread:74980 posi:14000242
-> Comparing positions: 1 with 0 has:219758
-> Only read nSites: 219758 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 77814
-> Sites to keep[12] from pop1: 77814
-> [readdata] lastread:77814 posi:14000242
-> Comparing positions: 1 with 0 has:297572
-> Only read nSites: 297572 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 68263
-> Sites to keep[16] from pop1: 68263
-> [readdata] lastread:68263 posi:14000242
-> Comparing positions: 1 with 0 has:365835
-> Only read nSites: 365835 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 56460
-> Sites to keep[17] from pop1: 56460
-> [readdata] lastread:56460 posi:14000242
-> Comparing positions: 1 with 0 has:422295
-> Only read nSites: 422295 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 63123
-> Sites to keep[18] from pop1: 63123
-> [readdata] lastread:63123 posi:14000242
-> Comparing positions: 1 with 0 has:485418
-> Only read nSites: 485418 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 50572
-> Sites to keep[19] from pop1: 50572
-> [readdata] lastread:50572 posi:14000242
-> Comparing positions: 1 with 0 has:535990
-> Only read nSites: 535990 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 60299
-> Sites to keep[2] from pop1: 60299
-> [readdata] lastread:60299 posi:14000242
-> Comparing positions: 1 with 0 has:596289
-> Only read nSites: 596289 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 60692
-> Sites to keep[20] from pop1: 60692
-> [readdata] lastread:60692 posi:14000242
-> Comparing positions: 1 with 0 has:656981
-> Only read nSites: 656981 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 51822
-> Sites to keep[3] from pop1: 51822
-> [readdata] lastread:51822 posi:14000242
-> Comparing positions: 1 with 0 has:708803
-> Only read nSites: 708803 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 72895
-> Sites to keep[4] from pop1: 72895
-> [readdata] lastread:72895 posi:14000242
-> Comparing positions: 1 with 0 has:781698
-> Only read nSites: 781698 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 72204
-> Sites to keep[5] from pop1: 72204
-> [readdata] lastread:72204 posi:14000242
-> Comparing positions: 1 with 0 has:853902
-> Only read nSites: 853902 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 73161
-> Sites to keep[6] from pop1: 73161
-> [readdata] lastread:73161 posi:14000242
-> Comparing positions: 1 with 0 has:927063
-> Only read nSites: 927063 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 66802
-> Sites to keep[7] from pop1: 66802
-> [readdata] lastread:66802 posi:14000242
-> Comparing positions: 1 with 0 has:993865
-> Only read nSites: 993865 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 63395
-> Sites to keep[8] from pop1: 63395
-> [readdata] lastread:63395 posi:14000242
-> Comparing positions: 1 with 0 has:1057260
-> Only read nSites: 1057260 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 75430
-> Sites to keep[9] from pop1: 75430
-> [readdata] lastread:75430 posi:14000242
-> Comparing positions: 1 with 0 has:1132690
-> Only read nSites: 1132690 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1132690
------------
startlik=-1917831.862715
lik[2]=-212019.335570 diff=1.705813e+06 alpha:1.000000 sr2:2.751823e-01
lik[5]=-107952.457098 diff=1.040669e+05 alpha:1.354203 sr2:1.222607e-02
lik[8]=-107796.242748 diff=1.562143e+02 alpha:1.884069 sr2:1.793755e-07
lik[11]=-107792.648386 diff=3.594361e+00 alpha:2.586955 sr2:3.139571e-10
lik[14]=-107785.007053 diff=7.641333e+00 alpha:4.000000 sr2:1.163626e-11
lik[17]=-107782.897637 diff=2.109417e+00 alpha:5.261490 sr2:2.658007e-11
lik[20]=-107781.987937 diff=9.096998e-01 alpha:3.094626 sr2:5.615945e-12
lik[23]=-107781.765670 diff=2.222667e-01 alpha:4.578733 sr2:2.860646e-12
-> Breaking EM(sr2) at iter:24, sqrt(sr2):7.730103e-07
likelihood: -107781.765670
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447020 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1430342
-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA06985.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 69774
-> Sites to keep[1] from pop1: 69774
-> [readdata] lastread:69774 posi:14000242
-> Comparing positions: 1 with 0 has:69774
-> Only read nSites: 69774 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 76796
-> Sites to keep[10] from pop1: 76796
-> [readdata] lastread:76796 posi:14000242
-> Comparing positions: 1 with 0 has:146570
-> Only read nSites: 146570 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 74325
-> Sites to keep[11] from pop1: 74325
-> [readdata] lastread:74325 posi:14000242
-> Comparing positions: 1 with 0 has:220895
-> Only read nSites: 220895 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 74117
-> Sites to keep[12] from pop1: 74117
-> [readdata] lastread:74117 posi:14000242
-> Comparing positions: 1 with 0 has:295012
-> Only read nSites: 295012 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 68851
-> Sites to keep[16] from pop1: 68851
-> [readdata] lastread:68851 posi:14000242
-> Comparing positions: 1 with 0 has:363863
-> Only read nSites: 363863 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 54545
-> Sites to keep[17] from pop1: 54545
-> [readdata] lastread:54545 posi:14000242
-> Comparing positions: 1 with 0 has:418408
-> Only read nSites: 418408 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 60856
-> Sites to keep[18] from pop1: 60856
-> [readdata] lastread:60856 posi:14000242
-> Comparing positions: 1 with 0 has:479264
-> Only read nSites: 479264 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 63845
-> Sites to keep[19] from pop1: 63845
-> [readdata] lastread:63845 posi:14000242
-> Comparing positions: 1 with 0 has:543109
-> Only read nSites: 543109 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 52778
-> Sites to keep[2] from pop1: 52778
-> [readdata] lastread:52778 posi:14000242
-> Comparing positions: 1 with 0 has:595887
-> Only read nSites: 595887 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 58258
-> Sites to keep[20] from pop1: 58258
-> [readdata] lastread:58258 posi:14000242
-> Comparing positions: 1 with 0 has:654145
-> Only read nSites: 654145 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 55585
-> Sites to keep[3] from pop1: 55585
-> [readdata] lastread:55585 posi:14000242
-> Comparing positions: 1 with 0 has:709730
-> Only read nSites: 709730 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 70234
-> Sites to keep[4] from pop1: 70234
-> [readdata] lastread:70234 posi:14000242
-> Comparing positions: 1 with 0 has:779964
-> Only read nSites: 779964 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 73629
-> Sites to keep[5] from pop1: 73629
-> [readdata] lastread:73629 posi:14000242
-> Comparing positions: 1 with 0 has:853593
-> Only read nSites: 853593 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 75387
-> Sites to keep[6] from pop1: 75387
-> [readdata] lastread:75387 posi:14000242
-> Comparing positions: 1 with 0 has:928980
-> Only read nSites: 928980 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 58902
-> Sites to keep[7] from pop1: 58902
-> [readdata] lastread:58902 posi:14000242
-> Comparing positions: 1 with 0 has:987882
-> Only read nSites: 987882 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 54431
-> Sites to keep[8] from pop1: 54431
-> [readdata] lastread:54431 posi:14000242
-> Comparing positions: 1 with 0 has:1042313
-> Only read nSites: 1042313 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 71271
-> Sites to keep[9] from pop1: 71271
-> [readdata] lastread:71271 posi:14000242
-> Comparing positions: 1 with 0 has:1113584
-> Only read nSites: 1113584 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1113584
------------
startlik=-3144465.367301
lik[2]=-203809.412276 diff=2.940656e+06 alpha:1.000000 sr2:4.358977e-01
lik[5]=-100455.267132 diff=1.033541e+05 alpha:1.363603 sr2:1.166902e-02
lik[8]=-100308.160988 diff=1.471061e+02 alpha:2.056727 sr2:6.938636e-08
lik[11]=-100274.419343 diff=3.374164e+01 alpha:3.069293 sr2:7.742072e-10
lik[14]=-100270.906852 diff=3.512491e+00 alpha:4.000000 sr2:2.141709e-10
lik[17]=-100270.892621 diff=1.423107e-02 alpha:1.567627 sr2:5.965016e-12
-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.069922e-07
likelihood: -100270.892621
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447022 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 74281
-> Sites to keep[1] from pop1: 74281
-> [readdata] lastread:74281 posi:14000284
-> Comparing positions: 1 with 0 has:74281
-> Only read nSites: 74281 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80883
-> Sites to keep[10] from pop1: 80883
-> [readdata] lastread:80883 posi:14000284
-> Comparing positions: 1 with 0 has:155164
-> Only read nSites: 155164 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 78959
-> Sites to keep[11] from pop1: 78959
-> [readdata] lastread:78959 posi:14000284
-> Comparing positions: 1 with 0 has:234123
-> Only read nSites: 234123 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 81390
-> Sites to keep[12] from pop1: 81390
-> [readdata] lastread:81390 posi:14000284
-> Comparing positions: 1 with 0 has:315513
-> Only read nSites: 315513 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 75359
-> Sites to keep[16] from pop1: 75359
-> [readdata] lastread:75359 posi:14000284
-> Comparing positions: 1 with 0 has:390872
-> Only read nSites: 390872 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 60991
-> Sites to keep[17] from pop1: 60991
-> [readdata] lastread:60991 posi:14000284
-> Comparing positions: 1 with 0 has:451863
-> Only read nSites: 451863 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 67633
-> Sites to keep[18] from pop1: 67633
-> [readdata] lastread:67633 posi:14000284
-> Comparing positions: 1 with 0 has:519496
-> Only read nSites: 519496 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 63775
-> Sites to keep[19] from pop1: 63775
-> [readdata] lastread:63775 posi:14000284
-> Comparing positions: 1 with 0 has:583271
-> Only read nSites: 583271 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 63598
-> Sites to keep[2] from pop1: 63598
-> [readdata] lastread:63598 posi:14000284
-> Comparing positions: 1 with 0 has:646869
-> Only read nSites: 646869 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 66596
-> Sites to keep[20] from pop1: 66596
-> [readdata] lastread:66596 posi:14000284
-> Comparing positions: 1 with 0 has:713465
-> Only read nSites: 713465 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 60197
-> Sites to keep[3] from pop1: 60197
-> [readdata] lastread:60197 posi:14000284
-> Comparing positions: 1 with 0 has:773662
-> Only read nSites: 773662 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 75423
-> Sites to keep[4] from pop1: 75423
-> [readdata] lastread:75423 posi:14000284
-> Comparing positions: 1 with 0 has:849085
-> Only read nSites: 849085 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 77747
-> Sites to keep[5] from pop1: 77747
-> [readdata] lastread:77747 posi:14000284
-> Comparing positions: 1 with 0 has:926832
-> Only read nSites: 926832 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 79340
-> Sites to keep[6] from pop1: 79340
-> [readdata] lastread:79340 posi:14000284
-> Comparing positions: 1 with 0 has:1006172
-> Only read nSites: 1006172 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 69929
-> Sites to keep[7] from pop1: 69929
-> [readdata] lastread:69929 posi:14000284
-> Comparing positions: 1 with 0 has:1076101
-> Only read nSites: 1076101 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 68114
-> Sites to keep[8] from pop1: 68114
-> [readdata] lastread:68114 posi:14000284
-> Comparing positions: 1 with 0 has:1144215
-> Only read nSites: 1144215 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 79185
-> Sites to keep[9] from pop1: 79185
-> [readdata] lastread:79185 posi:14000284
-> Comparing positions: 1 with 0 has:1223400
-> Only read nSites: 1223400 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1223400
------------
startlik=-1944250.671013
lik[2]=-137095.817852 diff=1.807155e+06 alpha:1.000000 sr2:5.592137e-01
lik[5]=-116235.474007 diff=2.086034e+04 alpha:1.318269 sr2:4.643012e-04
lik[8]=-116091.983570 diff=1.434904e+02 alpha:2.028033 sr2:5.949876e-08
lik[11]=-116051.717468 diff=4.026610e+01 alpha:4.000000 sr2:1.309146e-09
lik[14]=-116049.998647 diff=1.718821e+00 alpha:1.749292 sr2:1.838807e-10
lik[17]=-116049.948909 diff=4.973886e-02 alpha:4.158811 sr2:5.464500e-12
-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.107295e-07
likelihood: -116049.948909
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447024 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 73598
-> Sites to keep[1] from pop1: 73598
-> [readdata] lastread:73598 posi:14000242
-> Comparing positions: 1 with 0 has:73598
-> Only read nSites: 73598 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 79615
-> Sites to keep[10] from pop1: 79615
-> [readdata] lastread:79615 posi:14000242
-> Comparing positions: 1 with 0 has:153213
-> Only read nSites: 153213 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 78965
-> Sites to keep[11] from pop1: 78965
-> [readdata] lastread:78965 posi:14000242
-> Comparing positions: 1 with 0 has:232178
-> Only read nSites: 232178 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 80430
-> Sites to keep[12] from pop1: 80430
-> [readdata] lastread:80430 posi:14000242
-> Comparing positions: 1 with 0 has:312608
-> Only read nSites: 312608 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 73964
-> Sites to keep[16] from pop1: 73964
-> [readdata] lastread:73964 posi:14000242
-> Comparing positions: 1 with 0 has:386572
-> Only read nSites: 386572 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 61412
-> Sites to keep[17] from pop1: 61412
-> [readdata] lastread:61412 posi:14000242
-> Comparing positions: 1 with 0 has:447984
-> Only read nSites: 447984 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 67010
-> Sites to keep[18] from pop1: 67010
-> [readdata] lastread:67010 posi:14000242
-> Comparing positions: 1 with 0 has:514994
-> Only read nSites: 514994 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 60680
-> Sites to keep[19] from pop1: 60680
-> [readdata] lastread:60680 posi:14000242
-> Comparing positions: 1 with 0 has:575674
-> Only read nSites: 575674 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 63859
-> Sites to keep[2] from pop1: 63859
-> [readdata] lastread:63859 posi:14000242
-> Comparing positions: 1 with 0 has:639533
-> Only read nSites: 639533 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 66313
-> Sites to keep[20] from pop1: 66313
-> [readdata] lastread:66313 posi:14000242
-> Comparing positions: 1 with 0 has:705846
-> Only read nSites: 705846 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 59833
-> Sites to keep[3] from pop1: 59833
-> [readdata] lastread:59833 posi:14000242
-> Comparing positions: 1 with 0 has:765679
-> Only read nSites: 765679 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 75091
-> Sites to keep[4] from pop1: 75091
-> [readdata] lastread:75091 posi:14000242
-> Comparing positions: 1 with 0 has:840770
-> Only read nSites: 840770 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 76761
-> Sites to keep[5] from pop1: 76761
-> [readdata] lastread:76761 posi:14000242
-> Comparing positions: 1 with 0 has:917531
-> Only read nSites: 917531 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 78598
-> Sites to keep[6] from pop1: 78598
-> [readdata] lastread:78598 posi:14000242
-> Comparing positions: 1 with 0 has:996129
-> Only read nSites: 996129 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 69686
-> Sites to keep[7] from pop1: 69686
-> [readdata] lastread:69686 posi:14000242
-> Comparing positions: 1 with 0 has:1065815
-> Only read nSites: 1065815 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67420
-> Sites to keep[8] from pop1: 67420
-> [readdata] lastread:67420 posi:14000242
-> Comparing positions: 1 with 0 has:1133235
-> Only read nSites: 1133235 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 78847
-> Sites to keep[9] from pop1: 78847
-> [readdata] lastread:78847 posi:14000242
-> Comparing positions: 1 with 0 has:1212082
-> Only read nSites: 1212082 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1212082
------------
startlik=-2421411.166155
lik[2]=-149470.790177 diff=2.271940e+06 alpha:1.000000 sr2:5.452539e-01
lik[5]=-116430.011370 diff=3.304078e+04 alpha:1.256628 sr2:1.396633e-03
lik[8]=-116310.598512 diff=1.194129e+02 alpha:1.928593 sr2:1.000882e-07
lik[11]=-116253.434002 diff=5.716451e+01 alpha:4.000000 sr2:7.709330e-10
lik[14]=-116252.121485 diff=1.312516e+00 alpha:1.690889 sr2:2.242777e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):9.260033e-07
likelihood: -116252.121485
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447026 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 73533
-> Sites to keep[1] from pop1: 73533
-> [readdata] lastread:73533 posi:14000242
-> Comparing positions: 1 with 0 has:73533
-> Only read nSites: 73533 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 81312
-> Sites to keep[10] from pop1: 81312
-> [readdata] lastread:81312 posi:14000242
-> Comparing positions: 1 with 0 has:154845
-> Only read nSites: 154845 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 79290
-> Sites to keep[11] from pop1: 79290
-> [readdata] lastread:79290 posi:14000242
-> Comparing positions: 1 with 0 has:234135
-> Only read nSites: 234135 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 80039
-> Sites to keep[12] from pop1: 80039
-> [readdata] lastread:80039 posi:14000242
-> Comparing positions: 1 with 0 has:314174
-> Only read nSites: 314174 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 74922
-> Sites to keep[16] from pop1: 74922
-> [readdata] lastread:74922 posi:14000242
-> Comparing positions: 1 with 0 has:389096
-> Only read nSites: 389096 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 58587
-> Sites to keep[17] from pop1: 58587
-> [readdata] lastread:58587 posi:14000242
-> Comparing positions: 1 with 0 has:447683
-> Only read nSites: 447683 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 65566
-> Sites to keep[18] from pop1: 65566
-> [readdata] lastread:65566 posi:14000242
-> Comparing positions: 1 with 0 has:513249
-> Only read nSites: 513249 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 68729
-> Sites to keep[19] from pop1: 68729
-> [readdata] lastread:68729 posi:14000242
-> Comparing positions: 1 with 0 has:581978
-> Only read nSites: 581978 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 60752
-> Sites to keep[2] from pop1: 60752
-> [readdata] lastread:60752 posi:14000242
-> Comparing positions: 1 with 0 has:642730
-> Only read nSites: 642730 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 64309
-> Sites to keep[20] from pop1: 64309
-> [readdata] lastread:64309 posi:14000242
-> Comparing positions: 1 with 0 has:707039
-> Only read nSites: 707039 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 59382
-> Sites to keep[3] from pop1: 59382
-> [readdata] lastread:59382 posi:14000242
-> Comparing positions: 1 with 0 has:766421
-> Only read nSites: 766421 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 74753
-> Sites to keep[4] from pop1: 74753
-> [readdata] lastread:74753 posi:14000242
-> Comparing positions: 1 with 0 has:841174
-> Only read nSites: 841174 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 77685
-> Sites to keep[5] from pop1: 77685
-> [readdata] lastread:77685 posi:14000242
-> Comparing positions: 1 with 0 has:918859
-> Only read nSites: 918859 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 79752
-> Sites to keep[6] from pop1: 79752
-> [readdata] lastread:79752 posi:14000242
-> Comparing positions: 1 with 0 has:998611
-> Only read nSites: 998611 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 66492
-> Sites to keep[7] from pop1: 66492
-> [readdata] lastread:66492 posi:14000242
-> Comparing positions: 1 with 0 has:1065103
-> Only read nSites: 1065103 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 64997
-> Sites to keep[8] from pop1: 64997
-> [readdata] lastread:64997 posi:14000242
-> Comparing positions: 1 with 0 has:1130100
-> Only read nSites: 1130100 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 76239
-> Sites to keep[9] from pop1: 76239
-> [readdata] lastread:76239 posi:14000242
-> Comparing positions: 1 with 0 has:1206339
-> Only read nSites: 1206339 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1206339
------------
startlik=-2617243.196814
lik[2]=-134868.647270 diff=2.482375e+06 alpha:1.000000 sr2:6.784365e-01
lik[5]=-113878.724593 diff=2.098992e+04 alpha:1.246168 sr2:5.705902e-04
lik[8]=-113746.331007 diff=1.323936e+02 alpha:2.084066 sr2:5.282918e-08
lik[11]=-113735.963921 diff=1.036709e+01 alpha:3.808674 sr2:2.720190e-10
lik[14]=-113735.886056 diff=7.786481e-02 alpha:1.675212 sr2:2.997240e-11
-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.561609e-07
likelihood: -113735.886056
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07000.saf.idx is:2
-> Assuming .saf.gz file: smallNA07000.saf.gz
-> Assuming .saf.pos.gz: smallNA07000.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447027 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07000.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 75227
-> Sites to keep[1] from pop1: 75227
-> [readdata] lastread:75227 posi:14000242
-> Comparing positions: 1 with 0 has:75227
-> Only read nSites: 75227 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 82183
-> Sites to keep[10] from pop1: 82183
-> [readdata] lastread:82183 posi:14000242
-> Comparing positions: 1 with 0 has:157410
-> Only read nSites: 157410 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 80015
-> Sites to keep[11] from pop1: 80015
-> [readdata] lastread:80015 posi:14000242
-> Comparing positions: 1 with 0 has:237425
-> Only read nSites: 237425 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 81931
-> Sites to keep[12] from pop1: 81931
-> [readdata] lastread:81931 posi:14000242
-> Comparing positions: 1 with 0 has:319356
-> Only read nSites: 319356 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 76272
-> Sites to keep[16] from pop1: 76272
-> [readdata] lastread:76272 posi:14000242
-> Comparing positions: 1 with 0 has:395628
-> Only read nSites: 395628 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 61394
-> Sites to keep[17] from pop1: 61394
-> [readdata] lastread:61394 posi:14000242
-> Comparing positions: 1 with 0 has:457022
-> Only read nSites: 457022 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 67987
-> Sites to keep[18] from pop1: 67987
-> [readdata] lastread:67987 posi:14000242
-> Comparing positions: 1 with 0 has:525009
-> Only read nSites: 525009 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 67981
-> Sites to keep[19] from pop1: 67981
-> [readdata] lastread:67981 posi:14000242
-> Comparing positions: 1 with 0 has:592990
-> Only read nSites: 592990 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 63855
-> Sites to keep[2] from pop1: 63855
-> [readdata] lastread:63855 posi:14000242
-> Comparing positions: 1 with 0 has:656845
-> Only read nSites: 656845 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 67110
-> Sites to keep[20] from pop1: 67110
-> [readdata] lastread:67110 posi:14000242
-> Comparing positions: 1 with 0 has:723955
-> Only read nSites: 723955 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 60894
-> Sites to keep[3] from pop1: 60894
-> [readdata] lastread:60894 posi:14000242
-> Comparing positions: 1 with 0 has:784849
-> Only read nSites: 784849 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 76250
-> Sites to keep[4] from pop1: 76250
-> [readdata] lastread:76250 posi:14000242
-> Comparing positions: 1 with 0 has:861099
-> Only read nSites: 861099 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 78695
-> Sites to keep[5] from pop1: 78695
-> [readdata] lastread:78695 posi:14000242
-> Comparing positions: 1 with 0 has:939794
-> Only read nSites: 939794 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 80653
-> Sites to keep[6] from pop1: 80653
-> [readdata] lastread:80653 posi:14000242
-> Comparing positions: 1 with 0 has:1020447
-> Only read nSites: 1020447 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 70060
-> Sites to keep[7] from pop1: 70060
-> [readdata] lastread:70060 posi:14000242
-> Comparing positions: 1 with 0 has:1090507
-> Only read nSites: 1090507 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67896
-> Sites to keep[8] from pop1: 67896
-> [readdata] lastread:67896 posi:14000242
-> Comparing positions: 1 with 0 has:1158403
-> Only read nSites: 1158403 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 79989
-> Sites to keep[9] from pop1: 79989
-> [readdata] lastread:79989 posi:14000242
-> Comparing positions: 1 with 0 has:1238392
-> Only read nSites: 1238392 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1238392
------------
startlik=-2903772.017001
lik[2]=-212538.320171 diff=2.691234e+06 alpha:1.000000 sr2:4.746959e-01
lik[5]=-117607.934367 diff=9.493039e+04 alpha:1.387204 sr2:1.096166e-02
lik[8]=-117525.030184 diff=8.290418e+01 alpha:1.976138 sr2:5.219256e-08
lik[11]=-117511.752401 diff=1.327778e+01 alpha:2.650410 sr2:9.888159e-11
lik[14]=-117498.838357 diff=1.291404e+01 alpha:4.000000 sr2:1.445781e-10
lik[17]=-117498.583392 diff=2.549644e-01 alpha:1.678769 sr2:1.932188e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):9.287171e-07
likelihood: -117498.583392
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447029 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1451016
-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA07357.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 79381
-> Sites to keep[1] from pop1: 79381
-> [readdata] lastread:79381 posi:14000031
-> Comparing positions: 1 with 0 has:79381
-> Only read nSites: 79381 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80014
-> Sites to keep[10] from pop1: 80014
-> [readdata] lastread:80014 posi:14000031
-> Comparing positions: 1 with 0 has:159395
-> Only read nSites: 159395 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 80254
-> Sites to keep[11] from pop1: 80254
-> [readdata] lastread:80254 posi:14000031
-> Comparing positions: 1 with 0 has:239649
-> Only read nSites: 239649 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 84394
-> Sites to keep[12] from pop1: 84394
-> [readdata] lastread:84394 posi:14000031
-> Comparing positions: 1 with 0 has:324043
-> Only read nSites: 324043 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 77333
-> Sites to keep[16] from pop1: 77333
-> [readdata] lastread:77333 posi:14000031
-> Comparing positions: 1 with 0 has:401376
-> Only read nSites: 401376 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 68188
-> Sites to keep[17] from pop1: 68188
-> [readdata] lastread:68188 posi:14000031
-> Comparing positions: 1 with 0 has:469564
-> Only read nSites: 469564 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 71546
-> Sites to keep[18] from pop1: 71546
-> [readdata] lastread:71546 posi:14000031
-> Comparing positions: 1 with 0 has:541110
-> Only read nSites: 541110 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 58855
-> Sites to keep[19] from pop1: 58855
-> [readdata] lastread:58855 posi:14000031
-> Comparing positions: 1 with 0 has:599965
-> Only read nSites: 599965 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 74834
-> Sites to keep[2] from pop1: 74834
-> [readdata] lastread:74834 posi:14000031
-> Comparing positions: 1 with 0 has:674799
-> Only read nSites: 674799 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 75501
-> Sites to keep[20] from pop1: 75501
-> [readdata] lastread:75501 posi:14000031
-> Comparing positions: 1 with 0 has:750300
-> Only read nSites: 750300 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 65990
-> Sites to keep[3] from pop1: 65990
-> [readdata] lastread:65990 posi:14000031
-> Comparing positions: 1 with 0 has:816290
-> Only read nSites: 816290 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 77750
-> Sites to keep[4] from pop1: 77750
-> [readdata] lastread:77750 posi:14000031
-> Comparing positions: 1 with 0 has:894040
-> Only read nSites: 894040 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 77101
-> Sites to keep[5] from pop1: 77101
-> [readdata] lastread:77101 posi:14000031
-> Comparing positions: 1 with 0 has:971141
-> Only read nSites: 971141 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 79170
-> Sites to keep[6] from pop1: 79170
-> [readdata] lastread:79170 posi:14000031
-> Comparing positions: 1 with 0 has:1050311
-> Only read nSites: 1050311 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 77761
-> Sites to keep[7] from pop1: 77761
-> [readdata] lastread:77761 posi:14000031
-> Comparing positions: 1 with 0 has:1128072
-> Only read nSites: 1128072 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 75097
-> Sites to keep[8] from pop1: 75097
-> [readdata] lastread:75097 posi:14000031
-> Comparing positions: 1 with 0 has:1203169
-> Only read nSites: 1203169 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 81903
-> Sites to keep[9] from pop1: 81903
-> [readdata] lastread:81903 posi:14000031
-> Comparing positions: 1 with 0 has:1285072
-> Only read nSites: 1285072 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1285072
------------
startlik=-1794408.718876
lik[2]=-147811.306576 diff=1.646597e+06 alpha:1.000000 sr2:4.686174e-01
lik[5]=-114147.891244 diff=3.366342e+04 alpha:1.313253 sr2:1.093607e-03
lik[8]=-114067.444674 diff=8.044657e+01 alpha:1.894542 sr2:3.015563e-08
lik[11]=-113979.268163 diff=8.817651e+01 alpha:3.958229 sr2:6.341605e-10
lik[14]=-113975.929781 diff=3.338382e+00 alpha:2.145503 sr2:4.833900e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):8.995972e-07
likelihood: -113975.929781
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447031 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1451016
-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA11832.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 65834
-> Sites to keep[1] from pop1: 65834
-> [readdata] lastread:65834 posi:14000039
-> Comparing positions: 1 with 0 has:65834
-> Only read nSites: 65834 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 67839
-> Sites to keep[10] from pop1: 67839
-> [readdata] lastread:67839 posi:14000039
-> Comparing positions: 1 with 0 has:133673
-> Only read nSites: 133673 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 67467
-> Sites to keep[11] from pop1: 67467
-> [readdata] lastread:67467 posi:14000039
-> Comparing positions: 1 with 0 has:201140
-> Only read nSites: 201140 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 70181
-> Sites to keep[12] from pop1: 70181
-> [readdata] lastread:70181 posi:14000039
-> Comparing positions: 1 with 0 has:271321
-> Only read nSites: 271321 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 65392
-> Sites to keep[16] from pop1: 65392
-> [readdata] lastread:65392 posi:14000039
-> Comparing positions: 1 with 0 has:336713
-> Only read nSites: 336713 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 56025
-> Sites to keep[17] from pop1: 56025
-> [readdata] lastread:56025 posi:14000039
-> Comparing positions: 1 with 0 has:392738
-> Only read nSites: 392738 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 62408
-> Sites to keep[18] from pop1: 62408
-> [readdata] lastread:62408 posi:14000039
-> Comparing positions: 1 with 0 has:455146
-> Only read nSites: 455146 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 48380
-> Sites to keep[19] from pop1: 48380
-> [readdata] lastread:48380 posi:14000039
-> Comparing positions: 1 with 0 has:503526
-> Only read nSites: 503526 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 59771
-> Sites to keep[2] from pop1: 59771
-> [readdata] lastread:59771 posi:14000039
-> Comparing positions: 1 with 0 has:563297
-> Only read nSites: 563297 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 61741
-> Sites to keep[20] from pop1: 61741
-> [readdata] lastread:61741 posi:14000039
-> Comparing positions: 1 with 0 has:625038
-> Only read nSites: 625038 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 55909
-> Sites to keep[3] from pop1: 55909
-> [readdata] lastread:55909 posi:14000039
-> Comparing positions: 1 with 0 has:680947
-> Only read nSites: 680947 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 64971
-> Sites to keep[4] from pop1: 64971
-> [readdata] lastread:64971 posi:14000039
-> Comparing positions: 1 with 0 has:745918
-> Only read nSites: 745918 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 65152
-> Sites to keep[5] from pop1: 65152
-> [readdata] lastread:65152 posi:14000039
-> Comparing positions: 1 with 0 has:811070
-> Only read nSites: 811070 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 66888
-> Sites to keep[6] from pop1: 66888
-> [readdata] lastread:66888 posi:14000039
-> Comparing positions: 1 with 0 has:877958
-> Only read nSites: 877958 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 62147
-> Sites to keep[7] from pop1: 62147
-> [readdata] lastread:62147 posi:14000039
-> Comparing positions: 1 with 0 has:940105
-> Only read nSites: 940105 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 61136
-> Sites to keep[8] from pop1: 61136
-> [readdata] lastread:61136 posi:14000039
-> Comparing positions: 1 with 0 has:1001241
-> Only read nSites: 1001241 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 69267
-> Sites to keep[9] from pop1: 69267
-> [readdata] lastread:69267 posi:14000039
-> Comparing positions: 1 with 0 has:1070508
-> Only read nSites: 1070508 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1070508
------------
startlik=-1544698.378687
lik[2]=-180960.926092 diff=1.363737e+06 alpha:1.000000 sr2:3.222457e-01
lik[5]=-92787.225633 diff=8.817370e+04 alpha:1.513940 sr2:1.034810e-02
lik[8]=-92668.930184 diff=1.182954e+02 alpha:1.948587 sr2:3.248938e-08
lik[11]=-92612.573802 diff=5.635638e+01 alpha:4.000000 sr2:1.715035e-09
lik[14]=-92609.563578 diff=3.010224e+00 alpha:3.066773 sr2:2.698807e-10
lik[17]=-92609.240376 diff=3.232026e-01 alpha:2.809565 sr2:3.327699e-11
lik[20]=-92609.188796 diff=5.157970e-02 alpha:3.415162 sr2:4.101864e-12
-> Breaking EM(sr2) at iter:21, sqrt(sr2):7.646085e-07
likelihood: -92609.188796
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447034 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1451016
-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA06994.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 75596
-> Sites to keep[1] from pop1: 75596
-> [readdata] lastread:75596 posi:14000031
-> Comparing positions: 1 with 0 has:75596
-> Only read nSites: 75596 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 74626
-> Sites to keep[10] from pop1: 74626
-> [readdata] lastread:74626 posi:14000031
-> Comparing positions: 1 with 0 has:150222
-> Only read nSites: 150222 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 77200
-> Sites to keep[11] from pop1: 77200
-> [readdata] lastread:77200 posi:14000031
-> Comparing positions: 1 with 0 has:227422
-> Only read nSites: 227422 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 82626
-> Sites to keep[12] from pop1: 82626
-> [readdata] lastread:82626 posi:14000031
-> Comparing positions: 1 with 0 has:310048
-> Only read nSites: 310048 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 72139
-> Sites to keep[16] from pop1: 72139
-> [readdata] lastread:72139 posi:14000031
-> Comparing positions: 1 with 0 has:382187
-> Only read nSites: 382187 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 65110
-> Sites to keep[17] from pop1: 65110
-> [readdata] lastread:65110 posi:14000031
-> Comparing positions: 1 with 0 has:447297
-> Only read nSites: 447297 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 69166
-> Sites to keep[18] from pop1: 69166
-> [readdata] lastread:69166 posi:14000031
-> Comparing positions: 1 with 0 has:516463
-> Only read nSites: 516463 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 45083
-> Sites to keep[19] from pop1: 45083
-> [readdata] lastread:45083 posi:14000031
-> Comparing positions: 1 with 0 has:561546
-> Only read nSites: 561546 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 74993
-> Sites to keep[2] from pop1: 74993
-> [readdata] lastread:74993 posi:14000031
-> Comparing positions: 1 with 0 has:636539
-> Only read nSites: 636539 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 72748
-> Sites to keep[20] from pop1: 72748
-> [readdata] lastread:72748 posi:14000031
-> Comparing positions: 1 with 0 has:709287
-> Only read nSites: 709287 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 58761
-> Sites to keep[3] from pop1: 58761
-> [readdata] lastread:58761 posi:14000031
-> Comparing positions: 1 with 0 has:768048
-> Only read nSites: 768048 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 76694
-> Sites to keep[4] from pop1: 76694
-> [readdata] lastread:76694 posi:14000031
-> Comparing positions: 1 with 0 has:844742
-> Only read nSites: 844742 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 73174
-> Sites to keep[5] from pop1: 73174
-> [readdata] lastread:73174 posi:14000031
-> Comparing positions: 1 with 0 has:917916
-> Only read nSites: 917916 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 74017
-> Sites to keep[6] from pop1: 74017
-> [readdata] lastread:74017 posi:14000031
-> Comparing positions: 1 with 0 has:991933
-> Only read nSites: 991933 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 77444
-> Sites to keep[7] from pop1: 77444
-> [readdata] lastread:77444 posi:14000031
-> Comparing positions: 1 with 0 has:1069377
-> Only read nSites: 1069377 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 75514
-> Sites to keep[8] from pop1: 75514
-> [readdata] lastread:75514 posi:14000031
-> Comparing positions: 1 with 0 has:1144891
-> Only read nSites: 1144891 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 80999
-> Sites to keep[9] from pop1: 80999
-> [readdata] lastread:80999 posi:14000031
-> Comparing positions: 1 with 0 has:1225890
-> Only read nSites: 1225890 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1225890
------------
startlik=-2609878.940293
lik[2]=-263908.550811 diff=2.345970e+06 alpha:1.000000 sr2:2.866151e-01
lik[5]=-111817.357288 diff=1.520912e+05 alpha:1.338735 sr2:2.049943e-02
lik[8]=-111631.707535 diff=1.856498e+02 alpha:1.928003 sr2:6.535747e-08
lik[11]=-111602.284213 diff=2.942332e+01 alpha:3.685473 sr2:3.010232e-10
lik[14]=-111590.556964 diff=1.172725e+01 alpha:4.000000 sr2:1.622050e-10
lik[17]=-111590.305451 diff=2.515129e-01 alpha:2.035319 sr2:2.876033e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.687476e-07
likelihood: -111590.305451
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447036 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1451016
-> The choice of -nSites will require atleast: 55.351868 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA06985.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 77542
-> Sites to keep[1] from pop1: 77542
-> [readdata] lastread:77542 posi:14000031
-> Comparing positions: 1 with 0 has:77542
-> Only read nSites: 77542 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 79507
-> Sites to keep[10] from pop1: 79507
-> [readdata] lastread:79507 posi:14000031
-> Comparing positions: 1 with 0 has:157049
-> Only read nSites: 157049 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 80213
-> Sites to keep[11] from pop1: 80213
-> [readdata] lastread:80213 posi:14000031
-> Comparing positions: 1 with 0 has:237262
-> Only read nSites: 237262 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 78852
-> Sites to keep[12] from pop1: 78852
-> [readdata] lastread:78852 posi:14000031
-> Comparing positions: 1 with 0 has:316114
-> Only read nSites: 316114 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 76163
-> Sites to keep[16] from pop1: 76163
-> [readdata] lastread:76163 posi:14000031
-> Comparing positions: 1 with 0 has:392277
-> Only read nSites: 392277 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 66774
-> Sites to keep[17] from pop1: 66774
-> [readdata] lastread:66774 posi:14000031
-> Comparing positions: 1 with 0 has:459051
-> Only read nSites: 459051 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 75510
-> Sites to keep[18] from pop1: 75510
-> [readdata] lastread:75510 posi:14000031
-> Comparing positions: 1 with 0 has:534561
-> Only read nSites: 534561 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 63812
-> Sites to keep[19] from pop1: 63812
-> [readdata] lastread:63812 posi:14000031
-> Comparing positions: 1 with 0 has:598373
-> Only read nSites: 598373 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 66252
-> Sites to keep[2] from pop1: 66252
-> [readdata] lastread:66252 posi:14000031
-> Comparing positions: 1 with 0 has:664625
-> Only read nSites: 664625 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 74129
-> Sites to keep[20] from pop1: 74129
-> [readdata] lastread:74129 posi:14000031
-> Comparing positions: 1 with 0 has:738754
-> Only read nSites: 738754 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 70846
-> Sites to keep[3] from pop1: 70846
-> [readdata] lastread:70846 posi:14000031
-> Comparing positions: 1 with 0 has:809600
-> Only read nSites: 809600 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 74805
-> Sites to keep[4] from pop1: 74805
-> [readdata] lastread:74805 posi:14000031
-> Comparing positions: 1 with 0 has:884405
-> Only read nSites: 884405 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 79297
-> Sites to keep[5] from pop1: 79297
-> [readdata] lastread:79297 posi:14000031
-> Comparing positions: 1 with 0 has:963702
-> Only read nSites: 963702 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 79796
-> Sites to keep[6] from pop1: 79796
-> [readdata] lastread:79796 posi:14000031
-> Comparing positions: 1 with 0 has:1043498
-> Only read nSites: 1043498 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 68464
-> Sites to keep[7] from pop1: 68464
-> [readdata] lastread:68464 posi:14000031
-> Comparing positions: 1 with 0 has:1111962
-> Only read nSites: 1111962 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 64092
-> Sites to keep[8] from pop1: 64092
-> [readdata] lastread:64092 posi:14000031
-> Comparing positions: 1 with 0 has:1176054
-> Only read nSites: 1176054 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 76536
-> Sites to keep[9] from pop1: 76536
-> [readdata] lastread:76536 posi:14000031
-> Comparing positions: 1 with 0 has:1252590
-> Only read nSites: 1252590 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1252590
------------
startlik=-3085719.939659
lik[2]=-587610.418756 diff=2.498110e+06 alpha:1.000000 sr2:2.013279e-01
lik[5]=-107977.200304 diff=4.796332e+05 alpha:1.612123 sr2:1.148542e-01
lik[8]=-107741.704635 diff=2.354957e+02 alpha:2.310056 sr2:2.198900e-08
lik[11]=-107737.188747 diff=4.515888e+00 alpha:1.845853 sr2:4.659782e-10
lik[14]=-107736.942846 diff=2.459017e-01 alpha:4.000000 sr2:1.702622e-11
-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.839477e-07
likelihood: -107736.942846
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447038 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 82942
-> Sites to keep[1] from pop1: 82942
-> [readdata] lastread:82942 posi:14000031
-> Comparing positions: 1 with 0 has:82942
-> Only read nSites: 82942 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 82641
-> Sites to keep[10] from pop1: 82641
-> [readdata] lastread:82641 posi:14000031
-> Comparing positions: 1 with 0 has:165583
-> Only read nSites: 165583 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 84871
-> Sites to keep[11] from pop1: 84871
-> [readdata] lastread:84871 posi:14000031
-> Comparing positions: 1 with 0 has:250454
-> Only read nSites: 250454 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 87843
-> Sites to keep[12] from pop1: 87843
-> [readdata] lastread:87843 posi:14000031
-> Comparing positions: 1 with 0 has:338297
-> Only read nSites: 338297 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 83467
-> Sites to keep[16] from pop1: 83467
-> [readdata] lastread:83467 posi:14000031
-> Comparing positions: 1 with 0 has:421764
-> Only read nSites: 421764 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 75107
-> Sites to keep[17] from pop1: 75107
-> [readdata] lastread:75107 posi:14000031
-> Comparing positions: 1 with 0 has:496871
-> Only read nSites: 496871 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 79791
-> Sites to keep[18] from pop1: 79791
-> [readdata] lastread:79791 posi:14000031
-> Comparing positions: 1 with 0 has:576662
-> Only read nSites: 576662 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 63220
-> Sites to keep[19] from pop1: 63220
-> [readdata] lastread:63220 posi:14000031
-> Comparing positions: 1 with 0 has:639882
-> Only read nSites: 639882 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80683
-> Sites to keep[2] from pop1: 80683
-> [readdata] lastread:80683 posi:14000031
-> Comparing positions: 1 with 0 has:720565
-> Only read nSites: 720565 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 84130
-> Sites to keep[20] from pop1: 84130
-> [readdata] lastread:84130 posi:14000031
-> Comparing positions: 1 with 0 has:804695
-> Only read nSites: 804695 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 74121
-> Sites to keep[3] from pop1: 74121
-> [readdata] lastread:74121 posi:14000031
-> Comparing positions: 1 with 0 has:878816
-> Only read nSites: 878816 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80625
-> Sites to keep[4] from pop1: 80625
-> [readdata] lastread:80625 posi:14000031
-> Comparing positions: 1 with 0 has:959441
-> Only read nSites: 959441 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 82807
-> Sites to keep[5] from pop1: 82807
-> [readdata] lastread:82807 posi:14000031
-> Comparing positions: 1 with 0 has:1042248
-> Only read nSites: 1042248 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 83840
-> Sites to keep[6] from pop1: 83840
-> [readdata] lastread:83840 posi:14000031
-> Comparing positions: 1 with 0 has:1126088
-> Only read nSites: 1126088 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 83384
-> Sites to keep[7] from pop1: 83384
-> [readdata] lastread:83384 posi:14000031
-> Comparing positions: 1 with 0 has:1209472
-> Only read nSites: 1209472 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82617
-> Sites to keep[8] from pop1: 82617
-> [readdata] lastread:82617 posi:14000031
-> Comparing positions: 1 with 0 has:1292089
-> Only read nSites: 1292089 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 85706
-> Sites to keep[9] from pop1: 85706
-> [readdata] lastread:85706 posi:14000031
-> Comparing positions: 1 with 0 has:1377795
-> Only read nSites: 1377795 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1377795
------------
startlik=-2271202.460058
lik[2]=-181954.077744 diff=2.089248e+06 alpha:1.000000 sr2:4.396956e-01
lik[5]=-124876.199850 diff=5.707788e+04 alpha:1.306934 sr2:2.653606e-03
lik[8]=-124819.556120 diff=5.664373e+01 alpha:1.811621 sr2:3.878599e-08
lik[11]=-124806.061301 diff=1.349482e+01 alpha:2.870644 sr2:5.158721e-11
lik[14]=-124787.187352 diff=1.887395e+01 alpha:4.000000 sr2:7.355566e-11
lik[17]=-124787.072978 diff=1.143742e-01 alpha:2.389461 sr2:2.050937e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.890662e-07
likelihood: -124787.072978
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447040 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 82247
-> Sites to keep[1] from pop1: 82247
-> [readdata] lastread:82247 posi:14000031
-> Comparing positions: 1 with 0 has:82247
-> Only read nSites: 82247 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 81549
-> Sites to keep[10] from pop1: 81549
-> [readdata] lastread:81549 posi:14000031
-> Comparing positions: 1 with 0 has:163796
-> Only read nSites: 163796 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 85053
-> Sites to keep[11] from pop1: 85053
-> [readdata] lastread:85053 posi:14000031
-> Comparing positions: 1 with 0 has:248849
-> Only read nSites: 248849 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 86370
-> Sites to keep[12] from pop1: 86370
-> [readdata] lastread:86370 posi:14000031
-> Comparing positions: 1 with 0 has:335219
-> Only read nSites: 335219 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 81250
-> Sites to keep[16] from pop1: 81250
-> [readdata] lastread:81250 posi:14000031
-> Comparing positions: 1 with 0 has:416469
-> Only read nSites: 416469 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 75745
-> Sites to keep[17] from pop1: 75745
-> [readdata] lastread:75745 posi:14000031
-> Comparing positions: 1 with 0 has:492214
-> Only read nSites: 492214 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 79942
-> Sites to keep[18] from pop1: 79942
-> [readdata] lastread:79942 posi:14000031
-> Comparing positions: 1 with 0 has:572156
-> Only read nSites: 572156 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 60318
-> Sites to keep[19] from pop1: 60318
-> [readdata] lastread:60318 posi:14000031
-> Comparing positions: 1 with 0 has:632474
-> Only read nSites: 632474 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 81218
-> Sites to keep[2] from pop1: 81218
-> [readdata] lastread:81218 posi:14000031
-> Comparing positions: 1 with 0 has:713692
-> Only read nSites: 713692 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 83282
-> Sites to keep[20] from pop1: 83282
-> [readdata] lastread:83282 posi:14000031
-> Comparing positions: 1 with 0 has:796974
-> Only read nSites: 796974 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 74259
-> Sites to keep[3] from pop1: 74259
-> [readdata] lastread:74259 posi:14000031
-> Comparing positions: 1 with 0 has:871233
-> Only read nSites: 871233 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80665
-> Sites to keep[4] from pop1: 80665
-> [readdata] lastread:80665 posi:14000031
-> Comparing positions: 1 with 0 has:951898
-> Only read nSites: 951898 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 81846
-> Sites to keep[5] from pop1: 81846
-> [readdata] lastread:81846 posi:14000031
-> Comparing positions: 1 with 0 has:1033744
-> Only read nSites: 1033744 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 83193
-> Sites to keep[6] from pop1: 83193
-> [readdata] lastread:83193 posi:14000031
-> Comparing positions: 1 with 0 has:1116937
-> Only read nSites: 1116937 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 82836
-> Sites to keep[7] from pop1: 82836
-> [readdata] lastread:82836 posi:14000031
-> Comparing positions: 1 with 0 has:1199773
-> Only read nSites: 1199773 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 81919
-> Sites to keep[8] from pop1: 81919
-> [readdata] lastread:81919 posi:14000031
-> Comparing positions: 1 with 0 has:1281692
-> Only read nSites: 1281692 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 85249
-> Sites to keep[9] from pop1: 85249
-> [readdata] lastread:85249 posi:14000031
-> Comparing positions: 1 with 0 has:1366941
-> Only read nSites: 1366941 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1366941
------------
startlik=-2488003.407495
lik[2]=-179552.870898 diff=2.308451e+06 alpha:1.000000 sr2:5.110480e-01
lik[5]=-125258.053723 diff=5.429482e+04 alpha:1.330379 sr2:2.990583e-03
lik[8]=-125189.429417 diff=6.862431e+01 alpha:1.935059 sr2:2.703159e-08
lik[11]=-125158.670303 diff=3.075911e+01 alpha:4.000000 sr2:2.416857e-10
lik[14]=-125153.112392 diff=5.557911e+00 alpha:6.035875 sr2:2.493211e-10
lik[17]=-125152.654731 diff=4.576606e-01 alpha:2.003660 sr2:3.364268e-11
-> Breaking EM(sq2) at iter:19, sqrt(sq2):8.512737e-07
likelihood: -125152.654731
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447042 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 81981
-> Sites to keep[1] from pop1: 81981
-> [readdata] lastread:81981 posi:14000031
-> Comparing positions: 1 with 0 has:81981
-> Only read nSites: 81981 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 83185
-> Sites to keep[10] from pop1: 83185
-> [readdata] lastread:83185 posi:14000031
-> Comparing positions: 1 with 0 has:165166
-> Only read nSites: 165166 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 85115
-> Sites to keep[11] from pop1: 85115
-> [readdata] lastread:85115 posi:14000031
-> Comparing positions: 1 with 0 has:250281
-> Only read nSites: 250281 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 85529
-> Sites to keep[12] from pop1: 85529
-> [readdata] lastread:85529 posi:14000031
-> Comparing positions: 1 with 0 has:335810
-> Only read nSites: 335810 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 82619
-> Sites to keep[16] from pop1: 82619
-> [readdata] lastread:82619 posi:14000031
-> Comparing positions: 1 with 0 has:418429
-> Only read nSites: 418429 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 71277
-> Sites to keep[17] from pop1: 71277
-> [readdata] lastread:71277 posi:14000031
-> Comparing positions: 1 with 0 has:489706
-> Only read nSites: 489706 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 79258
-> Sites to keep[18] from pop1: 79258
-> [readdata] lastread:79258 posi:14000031
-> Comparing positions: 1 with 0 has:568964
-> Only read nSites: 568964 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 68159
-> Sites to keep[19] from pop1: 68159
-> [readdata] lastread:68159 posi:14000031
-> Comparing positions: 1 with 0 has:637123
-> Only read nSites: 637123 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 76419
-> Sites to keep[2] from pop1: 76419
-> [readdata] lastread:76419 posi:14000031
-> Comparing positions: 1 with 0 has:713542
-> Only read nSites: 713542 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 80370
-> Sites to keep[20] from pop1: 80370
-> [readdata] lastread:80370 posi:14000031
-> Comparing positions: 1 with 0 has:793912
-> Only read nSites: 793912 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 74240
-> Sites to keep[3] from pop1: 74240
-> [readdata] lastread:74240 posi:14000031
-> Comparing positions: 1 with 0 has:868152
-> Only read nSites: 868152 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80132
-> Sites to keep[4] from pop1: 80132
-> [readdata] lastread:80132 posi:14000031
-> Comparing positions: 1 with 0 has:948284
-> Only read nSites: 948284 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 83077
-> Sites to keep[5] from pop1: 83077
-> [readdata] lastread:83077 posi:14000031
-> Comparing positions: 1 with 0 has:1031361
-> Only read nSites: 1031361 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 84363
-> Sites to keep[6] from pop1: 84363
-> [readdata] lastread:84363 posi:14000031
-> Comparing positions: 1 with 0 has:1115724
-> Only read nSites: 1115724 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 78505
-> Sites to keep[7] from pop1: 78505
-> [readdata] lastread:78505 posi:14000031
-> Comparing positions: 1 with 0 has:1194229
-> Only read nSites: 1194229 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 77929
-> Sites to keep[8] from pop1: 77929
-> [readdata] lastread:77929 posi:14000031
-> Comparing positions: 1 with 0 has:1272158
-> Only read nSites: 1272158 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 81796
-> Sites to keep[9] from pop1: 81796
-> [readdata] lastread:81796 posi:14000031
-> Comparing positions: 1 with 0 has:1353954
-> Only read nSites: 1353954 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1353954
------------
startlik=-3231701.437761
lik[2]=-239931.268528 diff=2.991770e+06 alpha:1.000000 sr2:4.026887e-01
lik[5]=-122686.103044 diff=1.172452e+05 alpha:1.321706 sr2:1.099106e-02
lik[8]=-122602.084474 diff=8.401857e+01 alpha:1.799117 sr2:4.163378e-08
lik[11]=-122515.739594 diff=8.634488e+01 alpha:2.274726 sr2:2.885533e-10
lik[14]=-122502.856971 diff=1.288262e+01 alpha:4.000000 sr2:8.538622e-10
lik[17]=-122502.744676 diff=1.122952e-01 alpha:3.459023 sr2:1.312641e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.105827e-07
likelihood: -122502.744676
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11840.saf.idx is:2
-> Assuming .saf.gz file: smallNA11840.saf.gz
-> Assuming .saf.pos.gz: smallNA11840.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447044 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11840.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 84227
-> Sites to keep[1] from pop1: 84227
-> [readdata] lastread:84227 posi:14000031
-> Comparing positions: 1 with 0 has:84227
-> Only read nSites: 84227 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 84502
-> Sites to keep[10] from pop1: 84502
-> [readdata] lastread:84502 posi:14000031
-> Comparing positions: 1 with 0 has:168729
-> Only read nSites: 168729 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 86148
-> Sites to keep[11] from pop1: 86148
-> [readdata] lastread:86148 posi:14000031
-> Comparing positions: 1 with 0 has:254877
-> Only read nSites: 254877 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 88024
-> Sites to keep[12] from pop1: 88024
-> [readdata] lastread:88024 posi:14000031
-> Comparing positions: 1 with 0 has:342901
-> Only read nSites: 342901 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 84260
-> Sites to keep[16] from pop1: 84260
-> [readdata] lastread:84260 posi:14000031
-> Comparing positions: 1 with 0 has:427161
-> Only read nSites: 427161 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 75773
-> Sites to keep[17] from pop1: 75773
-> [readdata] lastread:75773 posi:14000031
-> Comparing positions: 1 with 0 has:502934
-> Only read nSites: 502934 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 82087
-> Sites to keep[18] from pop1: 82087
-> [readdata] lastread:82087 posi:14000031
-> Comparing positions: 1 with 0 has:585021
-> Only read nSites: 585021 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 67488
-> Sites to keep[19] from pop1: 67488
-> [readdata] lastread:67488 posi:14000031
-> Comparing positions: 1 with 0 has:652509
-> Only read nSites: 652509 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80648
-> Sites to keep[2] from pop1: 80648
-> [readdata] lastread:80648 posi:14000031
-> Comparing positions: 1 with 0 has:733157
-> Only read nSites: 733157 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 84730
-> Sites to keep[20] from pop1: 84730
-> [readdata] lastread:84730 posi:14000031
-> Comparing positions: 1 with 0 has:817887
-> Only read nSites: 817887 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 76155
-> Sites to keep[3] from pop1: 76155
-> [readdata] lastread:76155 posi:14000031
-> Comparing positions: 1 with 0 has:894042
-> Only read nSites: 894042 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 81795
-> Sites to keep[4] from pop1: 81795
-> [readdata] lastread:81795 posi:14000031
-> Comparing positions: 1 with 0 has:975837
-> Only read nSites: 975837 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 84459
-> Sites to keep[5] from pop1: 84459
-> [readdata] lastread:84459 posi:14000031
-> Comparing positions: 1 with 0 has:1060296
-> Only read nSites: 1060296 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 85614
-> Sites to keep[6] from pop1: 85614
-> [readdata] lastread:85614 posi:14000031
-> Comparing positions: 1 with 0 has:1145910
-> Only read nSites: 1145910 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 83307
-> Sites to keep[7] from pop1: 83307
-> [readdata] lastread:83307 posi:14000031
-> Comparing positions: 1 with 0 has:1229217
-> Only read nSites: 1229217 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82320
-> Sites to keep[8] from pop1: 82320
-> [readdata] lastread:82320 posi:14000031
-> Comparing positions: 1 with 0 has:1311537
-> Only read nSites: 1311537 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 86731
-> Sites to keep[9] from pop1: 86731
-> [readdata] lastread:86731 posi:14000031
-> Comparing positions: 1 with 0 has:1398268
-> Only read nSites: 1398268 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1398268
------------
startlik=-3942804.158771
lik[2]=-793500.114799 diff=3.149304e+06 alpha:1.000000 sr2:1.874626e-01
lik[5]=-128256.559951 diff=6.652436e+05 alpha:1.547820 sr2:1.652473e-01
lik[8]=-127251.064781 diff=1.005495e+03 alpha:1.348422 sr2:1.872819e-06
lik[11]=-127229.977098 diff=2.108768e+01 alpha:2.236674 sr2:7.426775e-10
lik[13]=-127137.923845 diff=9.205325e+01 alpha:1.000000 sr2:1.114477e-10
lik[16]=-126933.025487 diff=2.048984e+02 alpha:2.180740 sr2:2.186172e-09
lik[19]=-126928.184010 diff=4.841478e+00 alpha:3.262552 sr2:5.222961e-10
-> Breaking EM(sq2) at iter:21, sqrt(sq2):7.160827e-07
likelihood: -126928.184010
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447047 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1450698
-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA11832.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 68219
-> Sites to keep[1] from pop1: 68219
-> [readdata] lastread:68219 posi:14000039
-> Comparing positions: 1 with 0 has:68219
-> Only read nSites: 68219 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 71860
-> Sites to keep[10] from pop1: 71860
-> [readdata] lastread:71860 posi:14000039
-> Comparing positions: 1 with 0 has:140079
-> Only read nSites: 140079 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 70363
-> Sites to keep[11] from pop1: 70363
-> [readdata] lastread:70363 posi:14000039
-> Comparing positions: 1 with 0 has:210442
-> Only read nSites: 210442 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 73621
-> Sites to keep[12] from pop1: 73621
-> [readdata] lastread:73621 posi:14000039
-> Comparing positions: 1 with 0 has:284063
-> Only read nSites: 284063 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 66831
-> Sites to keep[16] from pop1: 66831
-> [readdata] lastread:66831 posi:14000039
-> Comparing positions: 1 with 0 has:350894
-> Only read nSites: 350894 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 56795
-> Sites to keep[17] from pop1: 56795
-> [readdata] lastread:56795 posi:14000039
-> Comparing positions: 1 with 0 has:407689
-> Only read nSites: 407689 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 60276
-> Sites to keep[18] from pop1: 60276
-> [readdata] lastread:60276 posi:14000039
-> Comparing positions: 1 with 0 has:467965
-> Only read nSites: 467965 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 55200
-> Sites to keep[19] from pop1: 55200
-> [readdata] lastread:55200 posi:14000039
-> Comparing positions: 1 with 0 has:523165
-> Only read nSites: 523165 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 60463
-> Sites to keep[2] from pop1: 60463
-> [readdata] lastread:60463 posi:14000039
-> Comparing positions: 1 with 0 has:583628
-> Only read nSites: 583628 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 60160
-> Sites to keep[20] from pop1: 60160
-> [readdata] lastread:60160 posi:14000039
-> Comparing positions: 1 with 0 has:643788
-> Only read nSites: 643788 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 54846
-> Sites to keep[3] from pop1: 54846
-> [readdata] lastread:54846 posi:14000039
-> Comparing positions: 1 with 0 has:698634
-> Only read nSites: 698634 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 68439
-> Sites to keep[4] from pop1: 68439
-> [readdata] lastread:68439 posi:14000039
-> Comparing positions: 1 with 0 has:767073
-> Only read nSites: 767073 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 68538
-> Sites to keep[5] from pop1: 68538
-> [readdata] lastread:68538 posi:14000039
-> Comparing positions: 1 with 0 has:835611
-> Only read nSites: 835611 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 69359
-> Sites to keep[6] from pop1: 69359
-> [readdata] lastread:69359 posi:14000039
-> Comparing positions: 1 with 0 has:904970
-> Only read nSites: 904970 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 64730
-> Sites to keep[7] from pop1: 64730
-> [readdata] lastread:64730 posi:14000039
-> Comparing positions: 1 with 0 has:969700
-> Only read nSites: 969700 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 62481
-> Sites to keep[8] from pop1: 62481
-> [readdata] lastread:62481 posi:14000039
-> Comparing positions: 1 with 0 has:1032181
-> Only read nSites: 1032181 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 72074
-> Sites to keep[9] from pop1: 72074
-> [readdata] lastread:72074 posi:14000039
-> Comparing positions: 1 with 0 has:1104255
-> Only read nSites: 1104255 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1104255
------------
startlik=-1821854.189524
lik[2]=-131781.657291 diff=1.690073e+06 alpha:1.000000 sr2:5.095267e-01
lik[5]=-99184.638437 diff=3.259702e+04 alpha:1.292208 sr2:1.575344e-03
lik[8]=-98989.342125 diff=1.952963e+02 alpha:2.052992 sr2:1.817951e-07
lik[11]=-98947.891227 diff=4.145090e+01 alpha:3.764934 sr2:8.204168e-10
lik[14]=-98935.090943 diff=1.280028e+01 alpha:4.000000 sr2:3.231456e-10
lik[17]=-98934.921864 diff=1.690791e-01 alpha:1.627681 sr2:7.059639e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):6.606225e-07
likelihood: -98934.921864
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447048 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1450698
-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA06994.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 79661
-> Sites to keep[1] from pop1: 79661
-> [readdata] lastread:79661 posi:14000031
-> Comparing positions: 1 with 0 has:79661
-> Only read nSites: 79661 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80696
-> Sites to keep[10] from pop1: 80696
-> [readdata] lastread:80696 posi:14000031
-> Comparing positions: 1 with 0 has:160357
-> Only read nSites: 160357 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 82817
-> Sites to keep[11] from pop1: 82817
-> [readdata] lastread:82817 posi:14000031
-> Comparing positions: 1 with 0 has:243174
-> Only read nSites: 243174 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 87375
-> Sites to keep[12] from pop1: 87375
-> [readdata] lastread:87375 posi:14000031
-> Comparing positions: 1 with 0 has:330549
-> Only read nSites: 330549 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 75683
-> Sites to keep[16] from pop1: 75683
-> [readdata] lastread:75683 posi:14000031
-> Comparing positions: 1 with 0 has:406232
-> Only read nSites: 406232 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 67739
-> Sites to keep[17] from pop1: 67739
-> [readdata] lastread:67739 posi:14000031
-> Comparing positions: 1 with 0 has:473971
-> Only read nSites: 473971 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 71399
-> Sites to keep[18] from pop1: 71399
-> [readdata] lastread:71399 posi:14000031
-> Comparing positions: 1 with 0 has:545370
-> Only read nSites: 545370 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 55591
-> Sites to keep[19] from pop1: 55591
-> [readdata] lastread:55591 posi:14000031
-> Comparing positions: 1 with 0 has:600961
-> Only read nSites: 600961 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 76518
-> Sites to keep[2] from pop1: 76518
-> [readdata] lastread:76518 posi:14000031
-> Comparing positions: 1 with 0 has:677479
-> Only read nSites: 677479 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 73458
-> Sites to keep[20] from pop1: 73458
-> [readdata] lastread:73458 posi:14000031
-> Comparing positions: 1 with 0 has:750937
-> Only read nSites: 750937 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 60770
-> Sites to keep[3] from pop1: 60770
-> [readdata] lastread:60770 posi:14000031
-> Comparing positions: 1 with 0 has:811707
-> Only read nSites: 811707 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 81018
-> Sites to keep[4] from pop1: 81018
-> [readdata] lastread:81018 posi:14000031
-> Comparing positions: 1 with 0 has:892725
-> Only read nSites: 892725 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 78936
-> Sites to keep[5] from pop1: 78936
-> [readdata] lastread:78936 posi:14000031
-> Comparing positions: 1 with 0 has:971661
-> Only read nSites: 971661 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 79384
-> Sites to keep[6] from pop1: 79384
-> [readdata] lastread:79384 posi:14000031
-> Comparing positions: 1 with 0 has:1051045
-> Only read nSites: 1051045 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 80730
-> Sites to keep[7] from pop1: 80730
-> [readdata] lastread:80730 posi:14000031
-> Comparing positions: 1 with 0 has:1131775
-> Only read nSites: 1131775 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 77459
-> Sites to keep[8] from pop1: 77459
-> [readdata] lastread:77459 posi:14000031
-> Comparing positions: 1 with 0 has:1209234
-> Only read nSites: 1209234 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 84562
-> Sites to keep[9] from pop1: 84562
-> [readdata] lastread:84562 posi:14000031
-> Comparing positions: 1 with 0 has:1293796
-> Only read nSites: 1293796 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1293796
------------
startlik=-2590286.072709
lik[2]=-176648.469412 diff=2.413638e+06 alpha:1.000000 sr2:4.969013e-01
lik[5]=-122261.740461 diff=5.438673e+04 alpha:1.274397 sr2:3.233830e-03
lik[8]=-122082.699761 diff=1.790407e+02 alpha:1.807499 sr2:1.150161e-07
lik[11]=-122010.993395 diff=7.170637e+01 alpha:2.562377 sr2:5.726600e-10
lik[14]=-122007.269540 diff=3.723855e+00 alpha:3.388067 sr2:3.597011e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.700450e-07
likelihood: -122007.269540
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447050 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1450698
-> The choice of -nSites will require atleast: 55.339737 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA06985.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 79157
-> Sites to keep[1] from pop1: 79157
-> [readdata] lastread:79157 posi:14000031
-> Comparing positions: 1 with 0 has:79157
-> Only read nSites: 79157 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 82709
-> Sites to keep[10] from pop1: 82709
-> [readdata] lastread:82709 posi:14000031
-> Comparing positions: 1 with 0 has:161866
-> Only read nSites: 161866 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 82354
-> Sites to keep[11] from pop1: 82354
-> [readdata] lastread:82354 posi:14000031
-> Comparing positions: 1 with 0 has:244220
-> Only read nSites: 244220 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 82389
-> Sites to keep[12] from pop1: 82389
-> [readdata] lastread:82389 posi:14000031
-> Comparing positions: 1 with 0 has:326609
-> Only read nSites: 326609 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 76194
-> Sites to keep[16] from pop1: 76194
-> [readdata] lastread:76194 posi:14000031
-> Comparing positions: 1 with 0 has:402803
-> Only read nSites: 402803 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 65045
-> Sites to keep[17] from pop1: 65045
-> [readdata] lastread:65045 posi:14000031
-> Comparing positions: 1 with 0 has:467848
-> Only read nSites: 467848 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 68449
-> Sites to keep[18] from pop1: 68449
-> [readdata] lastread:68449 posi:14000031
-> Comparing positions: 1 with 0 has:536297
-> Only read nSites: 536297 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 70447
-> Sites to keep[19] from pop1: 70447
-> [readdata] lastread:70447 posi:14000031
-> Comparing positions: 1 with 0 has:606744
-> Only read nSites: 606744 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 65694
-> Sites to keep[2] from pop1: 65694
-> [readdata] lastread:65694 posi:14000031
-> Comparing positions: 1 with 0 has:672438
-> Only read nSites: 672438 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 69991
-> Sites to keep[20] from pop1: 69991
-> [readdata] lastread:69991 posi:14000031
-> Comparing positions: 1 with 0 has:742429
-> Only read nSites: 742429 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 64812
-> Sites to keep[3] from pop1: 64812
-> [readdata] lastread:64812 posi:14000031
-> Comparing positions: 1 with 0 has:807241
-> Only read nSites: 807241 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 77745
-> Sites to keep[4] from pop1: 77745
-> [readdata] lastread:77745 posi:14000031
-> Comparing positions: 1 with 0 has:884986
-> Only read nSites: 884986 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 80328
-> Sites to keep[5] from pop1: 80328
-> [readdata] lastread:80328 posi:14000031
-> Comparing positions: 1 with 0 has:965314
-> Only read nSites: 965314 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 81945
-> Sites to keep[6] from pop1: 81945
-> [readdata] lastread:81945 posi:14000031
-> Comparing positions: 1 with 0 has:1047259
-> Only read nSites: 1047259 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 70214
-> Sites to keep[7] from pop1: 70214
-> [readdata] lastread:70214 posi:14000031
-> Comparing positions: 1 with 0 has:1117473
-> Only read nSites: 1117473 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 65001
-> Sites to keep[8] from pop1: 65001
-> [readdata] lastread:65001 posi:14000031
-> Comparing positions: 1 with 0 has:1182474
-> Only read nSites: 1182474 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 78606
-> Sites to keep[9] from pop1: 78606
-> [readdata] lastread:78606 posi:14000031
-> Comparing positions: 1 with 0 has:1261080
-> Only read nSites: 1261080 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1261080
------------
startlik=-3146092.518269
lik[2]=-169265.187354 diff=2.976827e+06 alpha:1.000000 sr2:5.932190e-01
lik[5]=-111984.696105 diff=5.728049e+04 alpha:1.314520 sr2:3.284890e-03
lik[8]=-111886.906405 diff=9.778970e+01 alpha:1.814452 sr2:4.946672e-08
lik[11]=-111856.838851 diff=3.006755e+01 alpha:4.000000 sr2:3.794339e-10
lik[14]=-111852.857571 diff=3.981279e+00 alpha:3.109304 sr2:2.133417e-10
lik[17]=-111852.822087 diff=3.548462e-02 alpha:1.860052 sr2:4.970159e-12
-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.221761e-07
likelihood: -111852.822087
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447052 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 85033
-> Sites to keep[1] from pop1: 85033
-> [readdata] lastread:85033 posi:14000031
-> Comparing positions: 1 with 0 has:85033
-> Only read nSites: 85033 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 87052
-> Sites to keep[10] from pop1: 87052
-> [readdata] lastread:87052 posi:14000031
-> Comparing positions: 1 with 0 has:172085
-> Only read nSites: 172085 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 87684
-> Sites to keep[11] from pop1: 87684
-> [readdata] lastread:87684 posi:14000031
-> Comparing positions: 1 with 0 has:259769
-> Only read nSites: 259769 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 91528
-> Sites to keep[12] from pop1: 91528
-> [readdata] lastread:91528 posi:14000031
-> Comparing positions: 1 with 0 has:351297
-> Only read nSites: 351297 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 83712
-> Sites to keep[16] from pop1: 83712
-> [readdata] lastread:83712 posi:14000031
-> Comparing positions: 1 with 0 has:435009
-> Only read nSites: 435009 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 74061
-> Sites to keep[17] from pop1: 74061
-> [readdata] lastread:74061 posi:14000031
-> Comparing positions: 1 with 0 has:509070
-> Only read nSites: 509070 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 76476
-> Sites to keep[18] from pop1: 76476
-> [readdata] lastread:76476 posi:14000031
-> Comparing positions: 1 with 0 has:585546
-> Only read nSites: 585546 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 70022
-> Sites to keep[19] from pop1: 70022
-> [readdata] lastread:70022 posi:14000031
-> Comparing positions: 1 with 0 has:655568
-> Only read nSites: 655568 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80800
-> Sites to keep[2] from pop1: 80800
-> [readdata] lastread:80800 posi:14000031
-> Comparing positions: 1 with 0 has:736368
-> Only read nSites: 736368 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 80634
-> Sites to keep[20] from pop1: 80634
-> [readdata] lastread:80634 posi:14000031
-> Comparing positions: 1 with 0 has:817002
-> Only read nSites: 817002 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 70951
-> Sites to keep[3] from pop1: 70951
-> [readdata] lastread:70951 posi:14000031
-> Comparing positions: 1 with 0 has:887953
-> Only read nSites: 887953 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 84276
-> Sites to keep[4] from pop1: 84276
-> [readdata] lastread:84276 posi:14000031
-> Comparing positions: 1 with 0 has:972229
-> Only read nSites: 972229 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 85025
-> Sites to keep[5] from pop1: 85025
-> [readdata] lastread:85025 posi:14000031
-> Comparing positions: 1 with 0 has:1057254
-> Only read nSites: 1057254 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 86319
-> Sites to keep[6] from pop1: 86319
-> [readdata] lastread:86319 posi:14000031
-> Comparing positions: 1 with 0 has:1143573
-> Only read nSites: 1143573 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 84745
-> Sites to keep[7] from pop1: 84745
-> [readdata] lastread:84745 posi:14000031
-> Comparing positions: 1 with 0 has:1228318
-> Only read nSites: 1228318 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 83173
-> Sites to keep[8] from pop1: 83173
-> [readdata] lastread:83173 posi:14000031
-> Comparing positions: 1 with 0 has:1311491
-> Only read nSites: 1311491 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 88383
-> Sites to keep[9] from pop1: 88383
-> [readdata] lastread:88383 posi:14000031
-> Comparing positions: 1 with 0 has:1399874
-> Only read nSites: 1399874 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1399874
------------
startlik=-1848187.957013
lik[2]=-146206.999388 diff=1.701981e+06 alpha:1.000000 sr2:4.956902e-01
lik[5]=-130940.586091 diff=1.526641e+04 alpha:1.246630 sr2:2.576683e-04
lik[8]=-130856.396941 diff=8.418915e+01 alpha:1.858708 sr2:1.468915e-08
lik[11]=-130843.028463 diff=1.336848e+01 alpha:4.000000 sr2:4.370370e-10
lik[14]=-130842.057742 diff=9.707210e-01 alpha:2.423033 sr2:7.808696e-11
-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.268921e-07
likelihood: -130842.057742
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447055 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 84077
-> Sites to keep[1] from pop1: 84077
-> [readdata] lastread:84077 posi:14000031
-> Comparing positions: 1 with 0 has:84077
-> Only read nSites: 84077 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 85955
-> Sites to keep[10] from pop1: 85955
-> [readdata] lastread:85955 posi:14000031
-> Comparing positions: 1 with 0 has:170032
-> Only read nSites: 170032 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 87604
-> Sites to keep[11] from pop1: 87604
-> [readdata] lastread:87604 posi:14000031
-> Comparing positions: 1 with 0 has:257636
-> Only read nSites: 257636 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 90327
-> Sites to keep[12] from pop1: 90327
-> [readdata] lastread:90327 posi:14000031
-> Comparing positions: 1 with 0 has:347963
-> Only read nSites: 347963 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 81979
-> Sites to keep[16] from pop1: 81979
-> [readdata] lastread:81979 posi:14000031
-> Comparing positions: 1 with 0 has:429942
-> Only read nSites: 429942 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 74666
-> Sites to keep[17] from pop1: 74666
-> [readdata] lastread:74666 posi:14000031
-> Comparing positions: 1 with 0 has:504608
-> Only read nSites: 504608 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 75940
-> Sites to keep[18] from pop1: 75940
-> [readdata] lastread:75940 posi:14000031
-> Comparing positions: 1 with 0 has:580548
-> Only read nSites: 580548 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 66915
-> Sites to keep[19] from pop1: 66915
-> [readdata] lastread:66915 posi:14000031
-> Comparing positions: 1 with 0 has:647463
-> Only read nSites: 647463 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 81092
-> Sites to keep[2] from pop1: 81092
-> [readdata] lastread:81092 posi:14000031
-> Comparing positions: 1 with 0 has:728555
-> Only read nSites: 728555 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 80491
-> Sites to keep[20] from pop1: 80491
-> [readdata] lastread:80491 posi:14000031
-> Comparing positions: 1 with 0 has:809046
-> Only read nSites: 809046 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 70503
-> Sites to keep[3] from pop1: 70503
-> [readdata] lastread:70503 posi:14000031
-> Comparing positions: 1 with 0 has:879549
-> Only read nSites: 879549 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 83833
-> Sites to keep[4] from pop1: 83833
-> [readdata] lastread:83833 posi:14000031
-> Comparing positions: 1 with 0 has:963382
-> Only read nSites: 963382 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 84054
-> Sites to keep[5] from pop1: 84054
-> [readdata] lastread:84054 posi:14000031
-> Comparing positions: 1 with 0 has:1047436
-> Only read nSites: 1047436 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 85646
-> Sites to keep[6] from pop1: 85646
-> [readdata] lastread:85646 posi:14000031
-> Comparing positions: 1 with 0 has:1133082
-> Only read nSites: 1133082 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 84573
-> Sites to keep[7] from pop1: 84573
-> [readdata] lastread:84573 posi:14000031
-> Comparing positions: 1 with 0 has:1217655
-> Only read nSites: 1217655 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82583
-> Sites to keep[8] from pop1: 82583
-> [readdata] lastread:82583 posi:14000031
-> Comparing positions: 1 with 0 has:1300238
-> Only read nSites: 1300238 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 88147
-> Sites to keep[9] from pop1: 88147
-> [readdata] lastread:88147 posi:14000031
-> Comparing positions: 1 with 0 has:1388385
-> Only read nSites: 1388385 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1388385
------------
startlik=-1886321.369441
lik[2]=-186871.082741 diff=1.699450e+06 alpha:1.000000 sr2:3.676728e-01
lik[5]=-132355.076861 diff=5.451601e+04 alpha:1.243059 sr2:1.985397e-03
lik[8]=-132172.619482 diff=1.824574e+02 alpha:1.850889 sr2:4.793345e-08
lik[11]=-132113.744048 diff=5.887543e+01 alpha:4.000000 sr2:2.056524e-09
lik[14]=-132105.840042 diff=7.904006e+00 alpha:2.137857 sr2:9.999016e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):8.422924e-07
likelihood: -132105.840042
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447057 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 83944
-> Sites to keep[1] from pop1: 83944
-> [readdata] lastread:83944 posi:14000031
-> Comparing positions: 1 with 0 has:83944
-> Only read nSites: 83944 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 87299
-> Sites to keep[10] from pop1: 87299
-> [readdata] lastread:87299 posi:14000031
-> Comparing positions: 1 with 0 has:171243
-> Only read nSites: 171243 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 87623
-> Sites to keep[11] from pop1: 87623
-> [readdata] lastread:87623 posi:14000031
-> Comparing positions: 1 with 0 has:258866
-> Only read nSites: 258866 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 89253
-> Sites to keep[12] from pop1: 89253
-> [readdata] lastread:89253 posi:14000031
-> Comparing positions: 1 with 0 has:348119
-> Only read nSites: 348119 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 82796
-> Sites to keep[16] from pop1: 82796
-> [readdata] lastread:82796 posi:14000031
-> Comparing positions: 1 with 0 has:430915
-> Only read nSites: 430915 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 70385
-> Sites to keep[17] from pop1: 70385
-> [readdata] lastread:70385 posi:14000031
-> Comparing positions: 1 with 0 has:501300
-> Only read nSites: 501300 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 73965
-> Sites to keep[18] from pop1: 73965
-> [readdata] lastread:73965 posi:14000031
-> Comparing positions: 1 with 0 has:575265
-> Only read nSites: 575265 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 76054
-> Sites to keep[19] from pop1: 76054
-> [readdata] lastread:76054 posi:14000031
-> Comparing positions: 1 with 0 has:651319
-> Only read nSites: 651319 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 76742
-> Sites to keep[2] from pop1: 76742
-> [readdata] lastread:76742 posi:14000031
-> Comparing positions: 1 with 0 has:728061
-> Only read nSites: 728061 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 77269
-> Sites to keep[20] from pop1: 77269
-> [readdata] lastread:77269 posi:14000031
-> Comparing positions: 1 with 0 has:805330
-> Only read nSites: 805330 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 69873
-> Sites to keep[3] from pop1: 69873
-> [readdata] lastread:69873 posi:14000031
-> Comparing positions: 1 with 0 has:875203
-> Only read nSites: 875203 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 83220
-> Sites to keep[4] from pop1: 83220
-> [readdata] lastread:83220 posi:14000031
-> Comparing positions: 1 with 0 has:958423
-> Only read nSites: 958423 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 84650
-> Sites to keep[5] from pop1: 84650
-> [readdata] lastread:84650 posi:14000031
-> Comparing positions: 1 with 0 has:1043073
-> Only read nSites: 1043073 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 86704
-> Sites to keep[6] from pop1: 86704
-> [readdata] lastread:86704 posi:14000031
-> Comparing positions: 1 with 0 has:1129777
-> Only read nSites: 1129777 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 79966
-> Sites to keep[7] from pop1: 79966
-> [readdata] lastread:79966 posi:14000031
-> Comparing positions: 1 with 0 has:1209743
-> Only read nSites: 1209743 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 78578
-> Sites to keep[8] from pop1: 78578
-> [readdata] lastread:78578 posi:14000031
-> Comparing positions: 1 with 0 has:1288321
-> Only read nSites: 1288321 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 84950
-> Sites to keep[9] from pop1: 84950
-> [readdata] lastread:84950 posi:14000031
-> Comparing positions: 1 with 0 has:1373271
-> Only read nSites: 1373271 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1373271
------------
startlik=-3008435.442488
lik[2]=-168636.962605 diff=2.839798e+06 alpha:1.000000 sr2:6.151854e-01
lik[5]=-128166.222531 diff=4.047074e+04 alpha:1.239474 sr2:1.659595e-03
lik[8]=-127977.418876 diff=1.888037e+02 alpha:1.868274 sr2:4.435244e-08
lik[11]=-127952.130261 diff=2.528862e+01 alpha:4.000000 sr2:1.218471e-09
lik[14]=-127950.503781 diff=1.626479e+00 alpha:2.300134 sr2:1.551907e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.735084e-07
likelihood: -127950.503781
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07357.saf.idx is:2
-> Assuming .saf.gz file: smallNA07357.saf.gz
-> Assuming .saf.pos.gz: smallNA07357.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447058 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07357.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 85926
-> Sites to keep[1] from pop1: 85926
-> [readdata] lastread:85926 posi:14000031
-> Comparing positions: 1 with 0 has:85926
-> Only read nSites: 85926 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 88436
-> Sites to keep[10] from pop1: 88436
-> [readdata] lastread:88436 posi:14000031
-> Comparing positions: 1 with 0 has:174362
-> Only read nSites: 174362 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 88674
-> Sites to keep[11] from pop1: 88674
-> [readdata] lastread:88674 posi:14000031
-> Comparing positions: 1 with 0 has:263036
-> Only read nSites: 263036 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 91928
-> Sites to keep[12] from pop1: 91928
-> [readdata] lastread:91928 posi:14000031
-> Comparing positions: 1 with 0 has:354964
-> Only read nSites: 354964 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 84540
-> Sites to keep[16] from pop1: 84540
-> [readdata] lastread:84540 posi:14000031
-> Comparing positions: 1 with 0 has:439504
-> Only read nSites: 439504 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 74555
-> Sites to keep[17] from pop1: 74555
-> [readdata] lastread:74555 posi:14000031
-> Comparing positions: 1 with 0 has:514059
-> Only read nSites: 514059 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 76938
-> Sites to keep[18] from pop1: 76938
-> [readdata] lastread:76938 posi:14000031
-> Comparing positions: 1 with 0 has:590997
-> Only read nSites: 590997 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 74990
-> Sites to keep[19] from pop1: 74990
-> [readdata] lastread:74990 posi:14000031
-> Comparing positions: 1 with 0 has:665987
-> Only read nSites: 665987 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 81004
-> Sites to keep[2] from pop1: 81004
-> [readdata] lastread:81004 posi:14000031
-> Comparing positions: 1 with 0 has:746991
-> Only read nSites: 746991 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 81098
-> Sites to keep[20] from pop1: 81098
-> [readdata] lastread:81098 posi:14000031
-> Comparing positions: 1 with 0 has:828089
-> Only read nSites: 828089 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 71841
-> Sites to keep[3] from pop1: 71841
-> [readdata] lastread:71841 posi:14000031
-> Comparing positions: 1 with 0 has:899930
-> Only read nSites: 899930 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 85086
-> Sites to keep[4] from pop1: 85086
-> [readdata] lastread:85086 posi:14000031
-> Comparing positions: 1 with 0 has:985016
-> Only read nSites: 985016 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 86159
-> Sites to keep[5] from pop1: 86159
-> [readdata] lastread:86159 posi:14000031
-> Comparing positions: 1 with 0 has:1071175
-> Only read nSites: 1071175 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 87609
-> Sites to keep[6] from pop1: 87609
-> [readdata] lastread:87609 posi:14000031
-> Comparing positions: 1 with 0 has:1158784
-> Only read nSites: 1158784 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 85044
-> Sites to keep[7] from pop1: 85044
-> [readdata] lastread:85044 posi:14000031
-> Comparing positions: 1 with 0 has:1243828
-> Only read nSites: 1243828 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82740
-> Sites to keep[8] from pop1: 82740
-> [readdata] lastread:82740 posi:14000031
-> Comparing positions: 1 with 0 has:1326568
-> Only read nSites: 1326568 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 89202
-> Sites to keep[9] from pop1: 89202
-> [readdata] lastread:89202 posi:14000031
-> Comparing positions: 1 with 0 has:1415770
-> Only read nSites: 1415770 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1415770
------------
startlik=-3459935.798266
lik[2]=-251740.852871 diff=3.208195e+06 alpha:1.000000 sr2:3.258789e-01
lik[5]=-132605.273308 diff=1.191356e+05 alpha:1.220661 sr2:1.109961e-02
lik[8]=-132398.511222 diff=2.067621e+02 alpha:1.670374 sr2:7.059395e-08
lik[11]=-132362.785570 diff=3.572565e+01 alpha:4.000000 sr2:1.464344e-09
lik[14]=-132360.644364 diff=2.141206e+00 alpha:2.470656 sr2:2.199634e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):6.396233e-07
likelihood: -132360.644364
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447061 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1372028
-> The choice of -nSites will require atleast: 52.338715 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA06994.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 65604
-> Sites to keep[1] from pop1: 65604
-> [readdata] lastread:65604 posi:14000039
-> Comparing positions: 1 with 0 has:65604
-> Only read nSites: 65604 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 67498
-> Sites to keep[10] from pop1: 67498
-> [readdata] lastread:67498 posi:14000039
-> Comparing positions: 1 with 0 has:133102
-> Only read nSites: 133102 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 67558
-> Sites to keep[11] from pop1: 67558
-> [readdata] lastread:67558 posi:14000039
-> Comparing positions: 1 with 0 has:200660
-> Only read nSites: 200660 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 72027
-> Sites to keep[12] from pop1: 72027
-> [readdata] lastread:72027 posi:14000039
-> Comparing positions: 1 with 0 has:272687
-> Only read nSites: 272687 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 63660
-> Sites to keep[16] from pop1: 63660
-> [readdata] lastread:63660 posi:14000039
-> Comparing positions: 1 with 0 has:336347
-> Only read nSites: 336347 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 54625
-> Sites to keep[17] from pop1: 54625
-> [readdata] lastread:54625 posi:14000039
-> Comparing positions: 1 with 0 has:390972
-> Only read nSites: 390972 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 58722
-> Sites to keep[18] from pop1: 58722
-> [readdata] lastread:58722 posi:14000039
-> Comparing positions: 1 with 0 has:449694
-> Only read nSites: 449694 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 43017
-> Sites to keep[19] from pop1: 43017
-> [readdata] lastread:43017 posi:14000039
-> Comparing positions: 1 with 0 has:492711
-> Only read nSites: 492711 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 60557
-> Sites to keep[2] from pop1: 60557
-> [readdata] lastread:60557 posi:14000039
-> Comparing positions: 1 with 0 has:553268
-> Only read nSites: 553268 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 58749
-> Sites to keep[20] from pop1: 58749
-> [readdata] lastread:58749 posi:14000039
-> Comparing positions: 1 with 0 has:612017
-> Only read nSites: 612017 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 49600
-> Sites to keep[3] from pop1: 49600
-> [readdata] lastread:49600 posi:14000039
-> Comparing positions: 1 with 0 has:661617
-> Only read nSites: 661617 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 67723
-> Sites to keep[4] from pop1: 67723
-> [readdata] lastread:67723 posi:14000039
-> Comparing positions: 1 with 0 has:729340
-> Only read nSites: 729340 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 65560
-> Sites to keep[5] from pop1: 65560
-> [readdata] lastread:65560 posi:14000039
-> Comparing positions: 1 with 0 has:794900
-> Only read nSites: 794900 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 65609
-> Sites to keep[6] from pop1: 65609
-> [readdata] lastread:65609 posi:14000039
-> Comparing positions: 1 with 0 has:860509
-> Only read nSites: 860509 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 64331
-> Sites to keep[7] from pop1: 64331
-> [readdata] lastread:64331 posi:14000039
-> Comparing positions: 1 with 0 has:924840
-> Only read nSites: 924840 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 62626
-> Sites to keep[8] from pop1: 62626
-> [readdata] lastread:62626 posi:14000039
-> Comparing positions: 1 with 0 has:987466
-> Only read nSites: 987466 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 70869
-> Sites to keep[9] from pop1: 70869
-> [readdata] lastread:70869 posi:14000039
-> Comparing positions: 1 with 0 has:1058335
-> Only read nSites: 1058335 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1058335
------------
startlik=-1579256.479162
lik[2]=-148502.319822 diff=1.430754e+06 alpha:1.000000 sr2:4.125705e-01
lik[5]=-97630.762370 diff=5.087156e+04 alpha:1.385374 sr2:3.541032e-03
lik[8]=-97448.683648 diff=1.820787e+02 alpha:1.970237 sr2:2.615860e-07
lik[11]=-97437.428149 diff=1.125550e+01 alpha:2.929593 sr2:6.757095e-10
lik[14]=-97411.734761 diff=2.569339e+01 alpha:4.000000 sr2:8.577351e-11
lik[17]=-97408.520565 diff=3.214195e+00 alpha:6.116832 sr2:1.754892e-10
lik[20]=-97408.429193 diff=9.137257e-02 alpha:1.487251 sr2:2.278726e-11
-> Breaking EM(sr2) at iter:21, sqrt(sr2):8.728496e-07
likelihood: -97408.429193
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447063 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1430342
-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA06985.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 65592
-> Sites to keep[1] from pop1: 65592
-> [readdata] lastread:65592 posi:14000039
-> Comparing positions: 1 with 0 has:65592
-> Only read nSites: 65592 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 70404
-> Sites to keep[10] from pop1: 70404
-> [readdata] lastread:70404 posi:14000039
-> Comparing positions: 1 with 0 has:135996
-> Only read nSites: 135996 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 68973
-> Sites to keep[11] from pop1: 68973
-> [readdata] lastread:68973 posi:14000039
-> Comparing positions: 1 with 0 has:204969
-> Only read nSites: 204969 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 69394
-> Sites to keep[12] from pop1: 69394
-> [readdata] lastread:69394 posi:14000039
-> Comparing positions: 1 with 0 has:274363
-> Only read nSites: 274363 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 64550
-> Sites to keep[16] from pop1: 64550
-> [readdata] lastread:64550 posi:14000039
-> Comparing positions: 1 with 0 has:338913
-> Only read nSites: 338913 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 53157
-> Sites to keep[17] from pop1: 53157
-> [readdata] lastread:53157 posi:14000039
-> Comparing positions: 1 with 0 has:392070
-> Only read nSites: 392070 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 60705
-> Sites to keep[18] from pop1: 60705
-> [readdata] lastread:60705 posi:14000039
-> Comparing positions: 1 with 0 has:452775
-> Only read nSites: 452775 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 56395
-> Sites to keep[19] from pop1: 56395
-> [readdata] lastread:56395 posi:14000039
-> Comparing positions: 1 with 0 has:509170
-> Only read nSites: 509170 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 52139
-> Sites to keep[2] from pop1: 52139
-> [readdata] lastread:52139 posi:14000039
-> Comparing positions: 1 with 0 has:561309
-> Only read nSites: 561309 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 57128
-> Sites to keep[20] from pop1: 57128
-> [readdata] lastread:57128 posi:14000039
-> Comparing positions: 1 with 0 has:618437
-> Only read nSites: 618437 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 54833
-> Sites to keep[3] from pop1: 54833
-> [readdata] lastread:54833 posi:14000039
-> Comparing positions: 1 with 0 has:673270
-> Only read nSites: 673270 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 65053
-> Sites to keep[4] from pop1: 65053
-> [readdata] lastread:65053 posi:14000039
-> Comparing positions: 1 with 0 has:738323
-> Only read nSites: 738323 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 67686
-> Sites to keep[5] from pop1: 67686
-> [readdata] lastread:67686 posi:14000039
-> Comparing positions: 1 with 0 has:806009
-> Only read nSites: 806009 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 69313
-> Sites to keep[6] from pop1: 69313
-> [readdata] lastread:69313 posi:14000039
-> Comparing positions: 1 with 0 has:875322
-> Only read nSites: 875322 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 56535
-> Sites to keep[7] from pop1: 56535
-> [readdata] lastread:56535 posi:14000039
-> Comparing positions: 1 with 0 has:931857
-> Only read nSites: 931857 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 53141
-> Sites to keep[8] from pop1: 53141
-> [readdata] lastread:53141 posi:14000039
-> Comparing positions: 1 with 0 has:984998
-> Only read nSites: 984998 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 66698
-> Sites to keep[9] from pop1: 66698
-> [readdata] lastread:66698 posi:14000039
-> Comparing positions: 1 with 0 has:1051696
-> Only read nSites: 1051696 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1051696
------------
startlik=-959754.499711
lik[2]=-147354.465796 diff=8.124000e+05 alpha:1.000000 sr2:2.335711e-01
lik[5]=-91046.938826 diff=5.630753e+04 alpha:1.444515 sr2:3.771919e-03
lik[8]=-90876.406838 diff=1.705320e+02 alpha:2.292567 sr2:1.067082e-07
lik[11]=-90838.475224 diff=3.793161e+01 alpha:4.000000 sr2:1.597088e-09
lik[14]=-90834.770263 diff=3.704961e+00 alpha:2.039586 sr2:4.375318e-10
lik[17]=-90830.834375 diff=3.935888e+00 alpha:3.523575 sr2:7.165565e-12
lik[20]=-90825.413355 diff=5.421020e+00 alpha:7.841349 sr2:2.328195e-11
lik[23]=-90824.931740 diff=4.816151e-01 alpha:1.917205 sr2:5.284856e-11
-> Breaking EM(sr2) at iter:24, sqrt(sr2):9.744032e-07
likelihood: -90824.931740
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447065 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 70531
-> Sites to keep[1] from pop1: 70531
-> [readdata] lastread:70531 posi:14000039
-> Comparing positions: 1 with 0 has:70531
-> Only read nSites: 70531 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 73266
-> Sites to keep[10] from pop1: 73266
-> [readdata] lastread:73266 posi:14000039
-> Comparing positions: 1 with 0 has:143797
-> Only read nSites: 143797 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 72998
-> Sites to keep[11] from pop1: 72998
-> [readdata] lastread:72998 posi:14000039
-> Comparing positions: 1 with 0 has:216795
-> Only read nSites: 216795 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 76026
-> Sites to keep[12] from pop1: 76026
-> [readdata] lastread:76026 posi:14000039
-> Comparing positions: 1 with 0 has:292821
-> Only read nSites: 292821 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 70953
-> Sites to keep[16] from pop1: 70953
-> [readdata] lastread:70953 posi:14000039
-> Comparing positions: 1 with 0 has:363774
-> Only read nSites: 363774 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 60429
-> Sites to keep[17] from pop1: 60429
-> [readdata] lastread:60429 posi:14000039
-> Comparing positions: 1 with 0 has:424203
-> Only read nSites: 424203 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 65658
-> Sites to keep[18] from pop1: 65658
-> [readdata] lastread:65658 posi:14000039
-> Comparing positions: 1 with 0 has:489861
-> Only read nSites: 489861 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 56521
-> Sites to keep[19] from pop1: 56521
-> [readdata] lastread:56521 posi:14000039
-> Comparing positions: 1 with 0 has:546382
-> Only read nSites: 546382 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 64153
-> Sites to keep[2] from pop1: 64153
-> [readdata] lastread:64153 posi:14000039
-> Comparing positions: 1 with 0 has:610535
-> Only read nSites: 610535 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 65712
-> Sites to keep[20] from pop1: 65712
-> [readdata] lastread:65712 posi:14000039
-> Comparing positions: 1 with 0 has:676247
-> Only read nSites: 676247 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 59336
-> Sites to keep[3] from pop1: 59336
-> [readdata] lastread:59336 posi:14000039
-> Comparing positions: 1 with 0 has:735583
-> Only read nSites: 735583 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 70487
-> Sites to keep[4] from pop1: 70487
-> [readdata] lastread:70487 posi:14000039
-> Comparing positions: 1 with 0 has:806070
-> Only read nSites: 806070 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 71634
-> Sites to keep[5] from pop1: 71634
-> [readdata] lastread:71634 posi:14000039
-> Comparing positions: 1 with 0 has:877704
-> Only read nSites: 877704 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 72519
-> Sites to keep[6] from pop1: 72519
-> [readdata] lastread:72519 posi:14000039
-> Comparing positions: 1 with 0 has:950223
-> Only read nSites: 950223 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 67913
-> Sites to keep[7] from pop1: 67913
-> [readdata] lastread:67913 posi:14000039
-> Comparing positions: 1 with 0 has:1018136
-> Only read nSites: 1018136 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67647
-> Sites to keep[8] from pop1: 67647
-> [readdata] lastread:67647 posi:14000039
-> Comparing positions: 1 with 0 has:1085783
-> Only read nSites: 1085783 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 74736
-> Sites to keep[9] from pop1: 74736
-> [readdata] lastread:74736 posi:14000039
-> Comparing positions: 1 with 0 has:1160519
-> Only read nSites: 1160519 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1160519
------------
startlik=-2422930.072517
lik[2]=-176387.612733 diff=2.246542e+06 alpha:1.000000 sr2:4.628494e-01
lik[5]=-106461.162235 diff=6.992645e+04 alpha:1.375322 sr2:5.694370e-03
lik[8]=-106223.559224 diff=2.376030e+02 alpha:1.817451 sr2:3.427114e-07
lik[11]=-106200.803639 diff=2.275559e+01 alpha:2.765950 sr2:9.153067e-10
lik[14]=-106166.487820 diff=3.431582e+01 alpha:4.000000 sr2:2.296494e-10
lik[17]=-106160.257759 diff=6.230061e+00 alpha:7.594570 sr2:3.148019e-10
lik[20]=-106159.478772 diff=7.789871e-01 alpha:1.666032 sr2:6.643910e-11
lik[23]=-106159.371722 diff=1.070497e-01 alpha:5.980628 sr2:5.628789e-12
-> Breaking EM(sr2) at iter:24, sqrt(sr2):3.599332e-07
likelihood: -106159.371722
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447068 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 70210
-> Sites to keep[1] from pop1: 70210
-> [readdata] lastread:70210 posi:14000039
-> Comparing positions: 1 with 0 has:70210
-> Only read nSites: 70210 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 72256
-> Sites to keep[10] from pop1: 72256
-> [readdata] lastread:72256 posi:14000039
-> Comparing positions: 1 with 0 has:142466
-> Only read nSites: 142466 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 73111
-> Sites to keep[11] from pop1: 73111
-> [readdata] lastread:73111 posi:14000039
-> Comparing positions: 1 with 0 has:215577
-> Only read nSites: 215577 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 75128
-> Sites to keep[12] from pop1: 75128
-> [readdata] lastread:75128 posi:14000039
-> Comparing positions: 1 with 0 has:290705
-> Only read nSites: 290705 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 69765
-> Sites to keep[16] from pop1: 69765
-> [readdata] lastread:69765 posi:14000039
-> Comparing positions: 1 with 0 has:360470
-> Only read nSites: 360470 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 61023
-> Sites to keep[17] from pop1: 61023
-> [readdata] lastread:61023 posi:14000039
-> Comparing positions: 1 with 0 has:421493
-> Only read nSites: 421493 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 65364
-> Sites to keep[18] from pop1: 65364
-> [readdata] lastread:65364 posi:14000039
-> Comparing positions: 1 with 0 has:486857
-> Only read nSites: 486857 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 54353
-> Sites to keep[19] from pop1: 54353
-> [readdata] lastread:54353 posi:14000039
-> Comparing positions: 1 with 0 has:541210
-> Only read nSites: 541210 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 64526
-> Sites to keep[2] from pop1: 64526
-> [readdata] lastread:64526 posi:14000039
-> Comparing positions: 1 with 0 has:605736
-> Only read nSites: 605736 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 64861
-> Sites to keep[20] from pop1: 64861
-> [readdata] lastread:64861 posi:14000039
-> Comparing positions: 1 with 0 has:670597
-> Only read nSites: 670597 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 59228
-> Sites to keep[3] from pop1: 59228
-> [readdata] lastread:59228 posi:14000039
-> Comparing positions: 1 with 0 has:729825
-> Only read nSites: 729825 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 70099
-> Sites to keep[4] from pop1: 70099
-> [readdata] lastread:70099 posi:14000039
-> Comparing positions: 1 with 0 has:799924
-> Only read nSites: 799924 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 71070
-> Sites to keep[5] from pop1: 71070
-> [readdata] lastread:71070 posi:14000039
-> Comparing positions: 1 with 0 has:870994
-> Only read nSites: 870994 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 71895
-> Sites to keep[6] from pop1: 71895
-> [readdata] lastread:71895 posi:14000039
-> Comparing positions: 1 with 0 has:942889
-> Only read nSites: 942889 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 67871
-> Sites to keep[7] from pop1: 67871
-> [readdata] lastread:67871 posi:14000039
-> Comparing positions: 1 with 0 has:1010760
-> Only read nSites: 1010760 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67025
-> Sites to keep[8] from pop1: 67025
-> [readdata] lastread:67025 posi:14000039
-> Comparing positions: 1 with 0 has:1077785
-> Only read nSites: 1077785 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 74243
-> Sites to keep[9] from pop1: 74243
-> [readdata] lastread:74243 posi:14000039
-> Comparing positions: 1 with 0 has:1152028
-> Only read nSites: 1152028 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1152028
------------
startlik=-1555050.379221
lik[2]=-164177.859285 diff=1.390873e+06 alpha:1.000000 sr2:3.677789e-01
lik[5]=-107592.441171 diff=5.658542e+04 alpha:1.448923 sr2:4.182989e-03
lik[8]=-107444.039592 diff=1.484016e+02 alpha:1.891677 sr2:2.049113e-07
lik[11]=-107407.162397 diff=3.687719e+01 alpha:3.150597 sr2:6.781163e-10
lik[14]=-107382.546291 diff=2.461611e+01 alpha:4.000000 sr2:5.091571e-10
lik[17]=-107382.254439 diff=2.918523e-01 alpha:2.172321 sr2:7.281920e-11
-> Breaking EM(sq2) at iter:19, sqrt(sq2):8.366895e-07
likelihood: -107382.254439
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447070 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 69587
-> Sites to keep[1] from pop1: 69587
-> [readdata] lastread:69587 posi:14000039
-> Comparing positions: 1 with 0 has:69587
-> Only read nSites: 69587 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 73686
-> Sites to keep[10] from pop1: 73686
-> [readdata] lastread:73686 posi:14000039
-> Comparing positions: 1 with 0 has:143273
-> Only read nSites: 143273 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 73237
-> Sites to keep[11] from pop1: 73237
-> [readdata] lastread:73237 posi:14000039
-> Comparing positions: 1 with 0 has:216510
-> Only read nSites: 216510 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 74250
-> Sites to keep[12] from pop1: 74250
-> [readdata] lastread:74250 posi:14000039
-> Comparing positions: 1 with 0 has:290760
-> Only read nSites: 290760 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 70161
-> Sites to keep[16] from pop1: 70161
-> [readdata] lastread:70161 posi:14000039
-> Comparing positions: 1 with 0 has:360921
-> Only read nSites: 360921 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 57350
-> Sites to keep[17] from pop1: 57350
-> [readdata] lastread:57350 posi:14000039
-> Comparing positions: 1 with 0 has:418271
-> Only read nSites: 418271 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 64237
-> Sites to keep[18] from pop1: 64237
-> [readdata] lastread:64237 posi:14000039
-> Comparing positions: 1 with 0 has:482508
-> Only read nSites: 482508 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 60424
-> Sites to keep[19] from pop1: 60424
-> [readdata] lastread:60424 posi:14000039
-> Comparing positions: 1 with 0 has:542932
-> Only read nSites: 542932 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 61272
-> Sites to keep[2] from pop1: 61272
-> [readdata] lastread:61272 posi:14000039
-> Comparing positions: 1 with 0 has:604204
-> Only read nSites: 604204 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 62410
-> Sites to keep[20] from pop1: 62410
-> [readdata] lastread:62410 posi:14000039
-> Comparing positions: 1 with 0 has:666614
-> Only read nSites: 666614 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 59022
-> Sites to keep[3] from pop1: 59022
-> [readdata] lastread:59022 posi:14000039
-> Comparing positions: 1 with 0 has:725636
-> Only read nSites: 725636 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 69479
-> Sites to keep[4] from pop1: 69479
-> [readdata] lastread:69479 posi:14000039
-> Comparing positions: 1 with 0 has:795115
-> Only read nSites: 795115 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 71656
-> Sites to keep[5] from pop1: 71656
-> [readdata] lastread:71656 posi:14000039
-> Comparing positions: 1 with 0 has:866771
-> Only read nSites: 866771 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 72825
-> Sites to keep[6] from pop1: 72825
-> [readdata] lastread:72825 posi:14000039
-> Comparing positions: 1 with 0 has:939596
-> Only read nSites: 939596 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 64297
-> Sites to keep[7] from pop1: 64297
-> [readdata] lastread:64297 posi:14000039
-> Comparing positions: 1 with 0 has:1003893
-> Only read nSites: 1003893 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 64074
-> Sites to keep[8] from pop1: 64074
-> [readdata] lastread:64074 posi:14000039
-> Comparing positions: 1 with 0 has:1067967
-> Only read nSites: 1067967 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 71999
-> Sites to keep[9] from pop1: 71999
-> [readdata] lastread:71999 posi:14000039
-> Comparing positions: 1 with 0 has:1139966
-> Only read nSites: 1139966 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1139966
------------
startlik=-1646319.755442
lik[2]=-163793.345212 diff=1.482526e+06 alpha:1.000000 sr2:4.088392e-01
lik[5]=-103789.272924 diff=6.000407e+04 alpha:1.493986 sr2:4.713342e-03
lik[8]=-103687.558845 diff=1.017141e+02 alpha:2.030312 sr2:9.474722e-08
lik[11]=-103658.400356 diff=2.915849e+01 alpha:3.326972 sr2:3.950915e-10
lik[14]=-103639.611159 diff=1.878920e+01 alpha:4.000000 sr2:3.920558e-10
lik[17]=-103639.379071 diff=2.320870e-01 alpha:2.189699 sr2:4.482582e-11
-> Breaking EM(sq2) at iter:19, sqrt(sq2):7.806008e-07
likelihood: -103639.379071
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11832.saf.idx is:2
-> Assuming .saf.gz file: smallNA11832.saf.gz
-> Assuming .saf.pos.gz: smallNA11832.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447072 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11832.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 71294
-> Sites to keep[1] from pop1: 71294
-> [readdata] lastread:71294 posi:14000039
-> Comparing positions: 1 with 0 has:71294
-> Only read nSites: 71294 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 74673
-> Sites to keep[10] from pop1: 74673
-> [readdata] lastread:74673 posi:14000039
-> Comparing positions: 1 with 0 has:145967
-> Only read nSites: 145967 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 74067
-> Sites to keep[11] from pop1: 74067
-> [readdata] lastread:74067 posi:14000039
-> Comparing positions: 1 with 0 has:220034
-> Only read nSites: 220034 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 76536
-> Sites to keep[12] from pop1: 76536
-> [readdata] lastread:76536 posi:14000039
-> Comparing positions: 1 with 0 has:296570
-> Only read nSites: 296570 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 71622
-> Sites to keep[16] from pop1: 71622
-> [readdata] lastread:71622 posi:14000039
-> Comparing positions: 1 with 0 has:368192
-> Only read nSites: 368192 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 60871
-> Sites to keep[17] from pop1: 60871
-> [readdata] lastread:60871 posi:14000039
-> Comparing positions: 1 with 0 has:429063
-> Only read nSites: 429063 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 66924
-> Sites to keep[18] from pop1: 66924
-> [readdata] lastread:66924 posi:14000039
-> Comparing positions: 1 with 0 has:495987
-> Only read nSites: 495987 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 60156
-> Sites to keep[19] from pop1: 60156
-> [readdata] lastread:60156 posi:14000039
-> Comparing positions: 1 with 0 has:556143
-> Only read nSites: 556143 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 64452
-> Sites to keep[2] from pop1: 64452
-> [readdata] lastread:64452 posi:14000039
-> Comparing positions: 1 with 0 has:620595
-> Only read nSites: 620595 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 66083
-> Sites to keep[20] from pop1: 66083
-> [readdata] lastread:66083 posi:14000039
-> Comparing positions: 1 with 0 has:686678
-> Only read nSites: 686678 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 60211
-> Sites to keep[3] from pop1: 60211
-> [readdata] lastread:60211 posi:14000039
-> Comparing positions: 1 with 0 has:746889
-> Only read nSites: 746889 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 71115
-> Sites to keep[4] from pop1: 71115
-> [readdata] lastread:71115 posi:14000039
-> Comparing positions: 1 with 0 has:818004
-> Only read nSites: 818004 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 72756
-> Sites to keep[5] from pop1: 72756
-> [readdata] lastread:72756 posi:14000039
-> Comparing positions: 1 with 0 has:890760
-> Only read nSites: 890760 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 73714
-> Sites to keep[6] from pop1: 73714
-> [readdata] lastread:73714 posi:14000039
-> Comparing positions: 1 with 0 has:964474
-> Only read nSites: 964474 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 68100
-> Sites to keep[7] from pop1: 68100
-> [readdata] lastread:68100 posi:14000039
-> Comparing positions: 1 with 0 has:1032574
-> Only read nSites: 1032574 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67345
-> Sites to keep[8] from pop1: 67345
-> [readdata] lastread:67345 posi:14000039
-> Comparing positions: 1 with 0 has:1099919
-> Only read nSites: 1099919 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 75341
-> Sites to keep[9] from pop1: 75341
-> [readdata] lastread:75341 posi:14000039
-> Comparing positions: 1 with 0 has:1175260
-> Only read nSites: 1175260 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1175260
------------
startlik=-2539802.144750
lik[2]=-194786.810758 diff=2.345015e+06 alpha:1.000000 sr2:4.234736e-01
lik[5]=-107563.040680 diff=8.722377e+04 alpha:1.478024 sr2:8.848660e-03
lik[8]=-107358.487277 diff=2.045534e+02 alpha:1.584769 sr2:1.521311e-07
lik[11]=-107331.279103 diff=2.720817e+01 alpha:3.283878 sr2:1.005785e-09
lik[14]=-107320.219953 diff=1.105915e+01 alpha:4.000000 sr2:2.364638e-10
lik[17]=-107320.154232 diff=6.572071e-02 alpha:2.080067 sr2:1.659644e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):3.623595e-07
likelihood: -107320.154232
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447074 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1430342
-> The choice of -nSites will require atleast: 54.563217 megabyte memory, that is at least: 0.01% of total memory
-> dim(smallNA06994.saf.idx):3
-> dim(smallNA06985.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 74424
-> Sites to keep[1] from pop1: 74424
-> [readdata] lastread:74424 posi:14000031
-> Comparing positions: 1 with 0 has:74424
-> Only read nSites: 74424 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 76419
-> Sites to keep[10] from pop1: 76419
-> [readdata] lastread:76419 posi:14000031
-> Comparing positions: 1 with 0 has:150843
-> Only read nSites: 150843 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 78580
-> Sites to keep[11] from pop1: 78580
-> [readdata] lastread:78580 posi:14000031
-> Comparing positions: 1 with 0 has:229423
-> Only read nSites: 229423 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 79896
-> Sites to keep[12] from pop1: 79896
-> [readdata] lastread:79896 posi:14000031
-> Comparing positions: 1 with 0 has:309319
-> Only read nSites: 309319 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 70251
-> Sites to keep[16] from pop1: 70251
-> [readdata] lastread:70251 posi:14000031
-> Comparing positions: 1 with 0 has:379570
-> Only read nSites: 379570 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 60545
-> Sites to keep[17] from pop1: 60545
-> [readdata] lastread:60545 posi:14000031
-> Comparing positions: 1 with 0 has:440115
-> Only read nSites: 440115 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 65819
-> Sites to keep[18] from pop1: 65819
-> [readdata] lastread:65819 posi:14000031
-> Comparing positions: 1 with 0 has:505934
-> Only read nSites: 505934 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 52107
-> Sites to keep[19] from pop1: 52107
-> [readdata] lastread:52107 posi:14000031
-> Comparing positions: 1 with 0 has:558041
-> Only read nSites: 558041 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 65076
-> Sites to keep[2] from pop1: 65076
-> [readdata] lastread:65076 posi:14000031
-> Comparing positions: 1 with 0 has:623117
-> Only read nSites: 623117 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 66504
-> Sites to keep[20] from pop1: 66504
-> [readdata] lastread:66504 posi:14000031
-> Comparing positions: 1 with 0 has:689621
-> Only read nSites: 689621 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 57387
-> Sites to keep[3] from pop1: 57387
-> [readdata] lastread:57387 posi:14000031
-> Comparing positions: 1 with 0 has:747008
-> Only read nSites: 747008 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 76413
-> Sites to keep[4] from pop1: 76413
-> [readdata] lastread:76413 posi:14000031
-> Comparing positions: 1 with 0 has:823421
-> Only read nSites: 823421 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 75707
-> Sites to keep[5] from pop1: 75707
-> [readdata] lastread:75707 posi:14000031
-> Comparing positions: 1 with 0 has:899128
-> Only read nSites: 899128 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 76306
-> Sites to keep[6] from pop1: 76306
-> [readdata] lastread:76306 posi:14000031
-> Comparing positions: 1 with 0 has:975434
-> Only read nSites: 975434 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 69269
-> Sites to keep[7] from pop1: 69269
-> [readdata] lastread:69269 posi:14000031
-> Comparing positions: 1 with 0 has:1044703
-> Only read nSites: 1044703 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 63966
-> Sites to keep[8] from pop1: 63966
-> [readdata] lastread:63966 posi:14000031
-> Comparing positions: 1 with 0 has:1108669
-> Only read nSites: 1108669 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 77174
-> Sites to keep[9] from pop1: 77174
-> [readdata] lastread:77174 posi:14000031
-> Comparing positions: 1 with 0 has:1185843
-> Only read nSites: 1185843 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1185843
------------
startlik=-3337134.849569
lik[2]=-206814.398100 diff=3.130320e+06 alpha:1.000000 sr2:4.018323e-01
lik[5]=-108462.936214 diff=9.835146e+04 alpha:1.294352 sr2:9.395940e-03
lik[8]=-108284.874805 diff=1.780614e+02 alpha:1.812501 sr2:1.284130e-07
lik[11]=-108246.987284 diff=3.788752e+01 alpha:2.939176 sr2:6.517346e-10
lik[14]=-108232.997485 diff=1.398980e+01 alpha:4.000000 sr2:2.783383e-10
lik[17]=-108232.732924 diff=2.645609e-01 alpha:2.163779 sr2:2.038712e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.980115e-07
likelihood: -108232.732924
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447076 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06994.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 81179
-> Sites to keep[1] from pop1: 81179
-> [readdata] lastread:81179 posi:14000031
-> Comparing positions: 1 with 0 has:81179
-> Only read nSites: 81179 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80756
-> Sites to keep[10] from pop1: 80756
-> [readdata] lastread:80756 posi:14000031
-> Comparing positions: 1 with 0 has:161935
-> Only read nSites: 161935 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 84131
-> Sites to keep[11] from pop1: 84131
-> [readdata] lastread:84131 posi:14000031
-> Comparing positions: 1 with 0 has:246066
-> Only read nSites: 246066 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 89463
-> Sites to keep[12] from pop1: 89463
-> [readdata] lastread:89463 posi:14000031
-> Comparing positions: 1 with 0 has:335529
-> Only read nSites: 335529 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 77977
-> Sites to keep[16] from pop1: 77977
-> [readdata] lastread:77977 posi:14000031
-> Comparing positions: 1 with 0 has:413506
-> Only read nSites: 413506 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 70531
-> Sites to keep[17] from pop1: 70531
-> [readdata] lastread:70531 posi:14000031
-> Comparing positions: 1 with 0 has:484037
-> Only read nSites: 484037 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 74033
-> Sites to keep[18] from pop1: 74033
-> [readdata] lastread:74033 posi:14000031
-> Comparing positions: 1 with 0 has:558070
-> Only read nSites: 558070 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 52794
-> Sites to keep[19] from pop1: 52794
-> [readdata] lastread:52794 posi:14000031
-> Comparing positions: 1 with 0 has:610864
-> Only read nSites: 610864 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80876
-> Sites to keep[2] from pop1: 80876
-> [readdata] lastread:80876 posi:14000031
-> Comparing positions: 1 with 0 has:691740
-> Only read nSites: 691740 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 77751
-> Sites to keep[20] from pop1: 77751
-> [readdata] lastread:77751 posi:14000031
-> Comparing positions: 1 with 0 has:769491
-> Only read nSites: 769491 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 63344
-> Sites to keep[3] from pop1: 63344
-> [readdata] lastread:63344 posi:14000031
-> Comparing positions: 1 with 0 has:832835
-> Only read nSites: 832835 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 83065
-> Sites to keep[4] from pop1: 83065
-> [readdata] lastread:83065 posi:14000031
-> Comparing positions: 1 with 0 has:915900
-> Only read nSites: 915900 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 80771
-> Sites to keep[5] from pop1: 80771
-> [readdata] lastread:80771 posi:14000031
-> Comparing positions: 1 with 0 has:996671
-> Only read nSites: 996671 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 80807
-> Sites to keep[6] from pop1: 80807
-> [readdata] lastread:80807 posi:14000031
-> Comparing positions: 1 with 0 has:1077478
-> Only read nSites: 1077478 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 84679
-> Sites to keep[7] from pop1: 84679
-> [readdata] lastread:84679 posi:14000031
-> Comparing positions: 1 with 0 has:1162157
-> Only read nSites: 1162157 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 83609
-> Sites to keep[8] from pop1: 83609
-> [readdata] lastread:83609 posi:14000031
-> Comparing positions: 1 with 0 has:1245766
-> Only read nSites: 1245766 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 87256
-> Sites to keep[9] from pop1: 87256
-> [readdata] lastread:87256 posi:14000031
-> Comparing positions: 1 with 0 has:1333022
-> Only read nSites: 1333022 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1333022
------------
startlik=-2245936.332820
lik[2]=-150555.138547 diff=2.095381e+06 alpha:1.000000 sr2:5.663306e-01
lik[5]=-129144.902382 diff=2.141024e+04 alpha:1.276161 sr2:4.818114e-04
lik[8]=-129002.682215 diff=1.422202e+02 alpha:1.919783 sr2:4.207822e-08
lik[11]=-128975.945483 diff=2.673673e+01 alpha:3.418160 sr2:4.316068e-10
lik[14]=-128975.676943 diff=2.685400e-01 alpha:1.672378 sr2:2.834219e-11
-> Breaking EM(sr2) at iter:15, sqrt(sr2):3.999003e-07
likelihood: -128975.676943
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447078 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06994.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 80460
-> Sites to keep[1] from pop1: 80460
-> [readdata] lastread:80460 posi:14000031
-> Comparing positions: 1 with 0 has:80460
-> Only read nSites: 80460 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 79746
-> Sites to keep[10] from pop1: 79746
-> [readdata] lastread:79746 posi:14000031
-> Comparing positions: 1 with 0 has:160206
-> Only read nSites: 160206 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 84053
-> Sites to keep[11] from pop1: 84053
-> [readdata] lastread:84053 posi:14000031
-> Comparing positions: 1 with 0 has:244259
-> Only read nSites: 244259 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 88448
-> Sites to keep[12] from pop1: 88448
-> [readdata] lastread:88448 posi:14000031
-> Comparing positions: 1 with 0 has:332707
-> Only read nSites: 332707 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 76751
-> Sites to keep[16] from pop1: 76751
-> [readdata] lastread:76751 posi:14000031
-> Comparing positions: 1 with 0 has:409458
-> Only read nSites: 409458 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 70621
-> Sites to keep[17] from pop1: 70621
-> [readdata] lastread:70621 posi:14000031
-> Comparing positions: 1 with 0 has:480079
-> Only read nSites: 480079 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 73629
-> Sites to keep[18] from pop1: 73629
-> [readdata] lastread:73629 posi:14000031
-> Comparing positions: 1 with 0 has:553708
-> Only read nSites: 553708 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 51131
-> Sites to keep[19] from pop1: 51131
-> [readdata] lastread:51131 posi:14000031
-> Comparing positions: 1 with 0 has:604839
-> Only read nSites: 604839 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80984
-> Sites to keep[2] from pop1: 80984
-> [readdata] lastread:80984 posi:14000031
-> Comparing positions: 1 with 0 has:685823
-> Only read nSites: 685823 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 77395
-> Sites to keep[20] from pop1: 77395
-> [readdata] lastread:77395 posi:14000031
-> Comparing positions: 1 with 0 has:763218
-> Only read nSites: 763218 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 62996
-> Sites to keep[3] from pop1: 62996
-> [readdata] lastread:62996 posi:14000031
-> Comparing positions: 1 with 0 has:826214
-> Only read nSites: 826214 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 82697
-> Sites to keep[4] from pop1: 82697
-> [readdata] lastread:82697 posi:14000031
-> Comparing positions: 1 with 0 has:908911
-> Only read nSites: 908911 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 79763
-> Sites to keep[5] from pop1: 79763
-> [readdata] lastread:79763 posi:14000031
-> Comparing positions: 1 with 0 has:988674
-> Only read nSites: 988674 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 80218
-> Sites to keep[6] from pop1: 80218
-> [readdata] lastread:80218 posi:14000031
-> Comparing positions: 1 with 0 has:1068892
-> Only read nSites: 1068892 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 84366
-> Sites to keep[7] from pop1: 84366
-> [readdata] lastread:84366 posi:14000031
-> Comparing positions: 1 with 0 has:1153258
-> Only read nSites: 1153258 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82592
-> Sites to keep[8] from pop1: 82592
-> [readdata] lastread:82592 posi:14000031
-> Comparing positions: 1 with 0 has:1235850
-> Only read nSites: 1235850 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 86996
-> Sites to keep[9] from pop1: 86996
-> [readdata] lastread:86996 posi:14000031
-> Comparing positions: 1 with 0 has:1322846
-> Only read nSites: 1322846 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1322846
------------
startlik=-2260757.228555
lik[2]=-167949.072329 diff=2.092808e+06 alpha:1.000000 sr2:4.641731e-01
lik[5]=-129142.306780 diff=3.880677e+04 alpha:1.244824 sr2:1.516323e-03
lik[8]=-129034.725342 diff=1.075814e+02 alpha:1.779596 sr2:6.871507e-08
lik[11]=-128984.141955 diff=5.058339e+01 alpha:4.000000 sr2:7.575351e-10
lik[14]=-128980.397269 diff=3.744686e+00 alpha:2.046281 sr2:4.053938e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):7.842853e-07
likelihood: -128980.397269
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447080 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06994.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 79354
-> Sites to keep[1] from pop1: 79354
-> [readdata] lastread:79354 posi:14000031
-> Comparing positions: 1 with 0 has:79354
-> Only read nSites: 79354 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 80791
-> Sites to keep[10] from pop1: 80791
-> [readdata] lastread:80791 posi:14000031
-> Comparing positions: 1 with 0 has:160145
-> Only read nSites: 160145 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 83718
-> Sites to keep[11] from pop1: 83718
-> [readdata] lastread:83718 posi:14000031
-> Comparing positions: 1 with 0 has:243863
-> Only read nSites: 243863 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 86870
-> Sites to keep[12] from pop1: 86870
-> [readdata] lastread:86870 posi:14000031
-> Comparing positions: 1 with 0 has:330733
-> Only read nSites: 330733 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 76683
-> Sites to keep[16] from pop1: 76683
-> [readdata] lastread:76683 posi:14000031
-> Comparing positions: 1 with 0 has:407416
-> Only read nSites: 407416 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 66497
-> Sites to keep[17] from pop1: 66497
-> [readdata] lastread:66497 posi:14000031
-> Comparing positions: 1 with 0 has:473913
-> Only read nSites: 473913 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 71300
-> Sites to keep[18] from pop1: 71300
-> [readdata] lastread:71300 posi:14000031
-> Comparing positions: 1 with 0 has:545213
-> Only read nSites: 545213 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 56159
-> Sites to keep[19] from pop1: 56159
-> [readdata] lastread:56159 posi:14000031
-> Comparing positions: 1 with 0 has:601372
-> Only read nSites: 601372 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 76395
-> Sites to keep[2] from pop1: 76395
-> [readdata] lastread:76395 posi:14000031
-> Comparing positions: 1 with 0 has:677767
-> Only read nSites: 677767 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 73705
-> Sites to keep[20] from pop1: 73705
-> [readdata] lastread:73705 posi:14000031
-> Comparing positions: 1 with 0 has:751472
-> Only read nSites: 751472 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 61886
-> Sites to keep[3] from pop1: 61886
-> [readdata] lastread:61886 posi:14000031
-> Comparing positions: 1 with 0 has:813358
-> Only read nSites: 813358 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 81864
-> Sites to keep[4] from pop1: 81864
-> [readdata] lastread:81864 posi:14000031
-> Comparing positions: 1 with 0 has:895222
-> Only read nSites: 895222 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 79878
-> Sites to keep[5] from pop1: 79878
-> [readdata] lastread:79878 posi:14000031
-> Comparing positions: 1 with 0 has:975100
-> Only read nSites: 975100 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 80579
-> Sites to keep[6] from pop1: 80579
-> [readdata] lastread:80579 posi:14000031
-> Comparing positions: 1 with 0 has:1055679
-> Only read nSites: 1055679 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 79656
-> Sites to keep[7] from pop1: 79656
-> [readdata] lastread:79656 posi:14000031
-> Comparing positions: 1 with 0 has:1135335
-> Only read nSites: 1135335 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 78417
-> Sites to keep[8] from pop1: 78417
-> [readdata] lastread:78417 posi:14000031
-> Comparing positions: 1 with 0 has:1213752
-> Only read nSites: 1213752 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 83272
-> Sites to keep[9] from pop1: 83272
-> [readdata] lastread:83272 posi:14000031
-> Comparing positions: 1 with 0 has:1297024
-> Only read nSites: 1297024 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1297024
------------
startlik=-3147294.702026
lik[2]=-158775.434570 diff=2.988519e+06 alpha:1.000000 sr2:6.146502e-01
lik[5]=-124237.828842 diff=3.453761e+04 alpha:1.257473 sr2:1.212065e-03
lik[8]=-124087.787923 diff=1.500409e+02 alpha:1.885581 sr2:6.293957e-08
lik[11]=-124052.672604 diff=3.511532e+01 alpha:4.000000 sr2:8.159472e-10
lik[14]=-124051.029895 diff=1.642709e+00 alpha:1.826935 sr2:1.419102e-10
lik[17]=-124050.998351 diff=3.154420e-02 alpha:4.026161 sr2:2.609979e-12
-> Breaking EM(sr2) at iter:18, sqrt(sr2):2.279282e-07
likelihood: -124050.998351
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06994.saf.idx is:2
-> Assuming .saf.gz file: smallNA06994.saf.gz
-> Assuming .saf.pos.gz: smallNA06994.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447083 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06994.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 81731
-> Sites to keep[1] from pop1: 81731
-> [readdata] lastread:81731 posi:14000031
-> Comparing positions: 1 with 0 has:81731
-> Only read nSites: 81731 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 82010
-> Sites to keep[10] from pop1: 82010
-> [readdata] lastread:82010 posi:14000031
-> Comparing positions: 1 with 0 has:163741
-> Only read nSites: 163741 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 85025
-> Sites to keep[11] from pop1: 85025
-> [readdata] lastread:85025 posi:14000031
-> Comparing positions: 1 with 0 has:248766
-> Only read nSites: 248766 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 89685
-> Sites to keep[12] from pop1: 89685
-> [readdata] lastread:89685 posi:14000031
-> Comparing positions: 1 with 0 has:338451
-> Only read nSites: 338451 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 78562
-> Sites to keep[16] from pop1: 78562
-> [readdata] lastread:78562 posi:14000031
-> Comparing positions: 1 with 0 has:417013
-> Only read nSites: 417013 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 70676
-> Sites to keep[17] from pop1: 70676
-> [readdata] lastread:70676 posi:14000031
-> Comparing positions: 1 with 0 has:487689
-> Only read nSites: 487689 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 74431
-> Sites to keep[18] from pop1: 74431
-> [readdata] lastread:74431 posi:14000031
-> Comparing positions: 1 with 0 has:562120
-> Only read nSites: 562120 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 55907
-> Sites to keep[19] from pop1: 55907
-> [readdata] lastread:55907 posi:14000031
-> Comparing positions: 1 with 0 has:618027
-> Only read nSites: 618027 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 80786
-> Sites to keep[2] from pop1: 80786
-> [readdata] lastread:80786 posi:14000031
-> Comparing positions: 1 with 0 has:698813
-> Only read nSites: 698813 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 78005
-> Sites to keep[20] from pop1: 78005
-> [readdata] lastread:78005 posi:14000031
-> Comparing positions: 1 with 0 has:776818
-> Only read nSites: 776818 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 63794
-> Sites to keep[3] from pop1: 63794
-> [readdata] lastread:63794 posi:14000031
-> Comparing positions: 1 with 0 has:840612
-> Only read nSites: 840612 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 83738
-> Sites to keep[4] from pop1: 83738
-> [readdata] lastread:83738 posi:14000031
-> Comparing positions: 1 with 0 has:924350
-> Only read nSites: 924350 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 81469
-> Sites to keep[5] from pop1: 81469
-> [readdata] lastread:81469 posi:14000031
-> Comparing positions: 1 with 0 has:1005819
-> Only read nSites: 1005819 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 81459
-> Sites to keep[6] from pop1: 81459
-> [readdata] lastread:81459 posi:14000031
-> Comparing positions: 1 with 0 has:1087278
-> Only read nSites: 1087278 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 84578
-> Sites to keep[7] from pop1: 84578
-> [readdata] lastread:84578 posi:14000031
-> Comparing positions: 1 with 0 has:1171856
-> Only read nSites: 1171856 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 82764
-> Sites to keep[8] from pop1: 82764
-> [readdata] lastread:82764 posi:14000031
-> Comparing positions: 1 with 0 has:1254620
-> Only read nSites: 1254620 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 87908
-> Sites to keep[9] from pop1: 87908
-> [readdata] lastread:87908 posi:14000031
-> Comparing positions: 1 with 0 has:1342528
-> Only read nSites: 1342528 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1342528
------------
startlik=-2303670.373896
lik[2]=-154107.766459 diff=2.149563e+06 alpha:1.000000 sr2:5.555697e-01
lik[5]=-130115.913079 diff=2.399185e+04 alpha:1.284821 sr2:6.620637e-04
lik[8]=-129908.505184 diff=2.074079e+02 alpha:1.959218 sr2:4.941965e-08
lik[11]=-129883.229122 diff=2.527606e+01 alpha:3.787946 sr2:2.190879e-09
lik[14]=-129882.570332 diff=6.587905e-01 alpha:2.551175 sr2:9.331378e-11
-> Breaking EM(sr2) at iter:15, sqrt(sr2):5.346436e-07
likelihood: -129882.570332
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447085 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06985.saf.idx):3
-> dim(smallNA11831.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 82607
-> Sites to keep[1] from pop1: 82607
-> [readdata] lastread:82607 posi:14000031
-> Comparing positions: 1 with 0 has:82607
-> Only read nSites: 82607 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 85506
-> Sites to keep[10] from pop1: 85506
-> [readdata] lastread:85506 posi:14000031
-> Comparing positions: 1 with 0 has:168113
-> Only read nSites: 168113 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 86784
-> Sites to keep[11] from pop1: 86784
-> [readdata] lastread:86784 posi:14000031
-> Comparing positions: 1 with 0 has:254897
-> Only read nSites: 254897 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 85135
-> Sites to keep[12] from pop1: 85135
-> [readdata] lastread:85135 posi:14000031
-> Comparing positions: 1 with 0 has:340032
-> Only read nSites: 340032 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 82353
-> Sites to keep[16] from pop1: 82353
-> [readdata] lastread:82353 posi:14000031
-> Comparing positions: 1 with 0 has:422385
-> Only read nSites: 422385 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 71667
-> Sites to keep[17] from pop1: 71667
-> [readdata] lastread:71667 posi:14000031
-> Comparing positions: 1 with 0 has:494052
-> Only read nSites: 494052 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 76797
-> Sites to keep[18] from pop1: 76797
-> [readdata] lastread:76797 posi:14000031
-> Comparing positions: 1 with 0 has:570849
-> Only read nSites: 570849 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 73273
-> Sites to keep[19] from pop1: 73273
-> [readdata] lastread:73273 posi:14000031
-> Comparing positions: 1 with 0 has:644122
-> Only read nSites: 644122 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 70211
-> Sites to keep[2] from pop1: 70211
-> [readdata] lastread:70211 posi:14000031
-> Comparing positions: 1 with 0 has:714333
-> Only read nSites: 714333 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 78457
-> Sites to keep[20] from pop1: 78457
-> [readdata] lastread:78457 posi:14000031
-> Comparing positions: 1 with 0 has:792790
-> Only read nSites: 792790 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 72294
-> Sites to keep[3] from pop1: 72294
-> [readdata] lastread:72294 posi:14000031
-> Comparing positions: 1 with 0 has:865084
-> Only read nSites: 865084 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80455
-> Sites to keep[4] from pop1: 80455
-> [readdata] lastread:80455 posi:14000031
-> Comparing positions: 1 with 0 has:945539
-> Only read nSites: 945539 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 86171
-> Sites to keep[5] from pop1: 86171
-> [readdata] lastread:86171 posi:14000031
-> Comparing positions: 1 with 0 has:1031710
-> Only read nSites: 1031710 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 86617
-> Sites to keep[6] from pop1: 86617
-> [readdata] lastread:86617 posi:14000031
-> Comparing positions: 1 with 0 has:1118327
-> Only read nSites: 1118327 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 75293
-> Sites to keep[7] from pop1: 75293
-> [readdata] lastread:75293 posi:14000031
-> Comparing positions: 1 with 0 has:1193620
-> Only read nSites: 1193620 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 71241
-> Sites to keep[8] from pop1: 71241
-> [readdata] lastread:71241 posi:14000031
-> Comparing positions: 1 with 0 has:1264861
-> Only read nSites: 1264861 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 81935
-> Sites to keep[9] from pop1: 81935
-> [readdata] lastread:81935 posi:14000031
-> Comparing positions: 1 with 0 has:1346796
-> Only read nSites: 1346796 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1346796
------------
startlik=-2514096.535974
lik[2]=-178971.317445 diff=2.335125e+06 alpha:1.000000 sr2:4.662374e-01
lik[5]=-122255.290953 diff=5.671603e+04 alpha:1.297006 sr2:2.743430e-03
lik[8]=-122141.624950 diff=1.136660e+02 alpha:1.810544 sr2:5.471750e-08
lik[11]=-122098.811890 diff=4.281306e+01 alpha:4.000000 sr2:5.567604e-10
lik[14]=-122089.609054 diff=9.202836e+00 alpha:2.592988 sr2:3.855811e-10
lik[17]=-122089.505301 diff=1.037531e-01 alpha:2.359254 sr2:1.047160e-11
-> Breaking EM(sr2) at iter:18, sqrt(sr2):4.127705e-07
likelihood: -122089.505301
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447087 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06985.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 81928
-> Sites to keep[1] from pop1: 81928
-> [readdata] lastread:81928 posi:14000031
-> Comparing positions: 1 with 0 has:81928
-> Only read nSites: 81928 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 84173
-> Sites to keep[10] from pop1: 84173
-> [readdata] lastread:84173 posi:14000031
-> Comparing positions: 1 with 0 has:166101
-> Only read nSites: 166101 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 86972
-> Sites to keep[11] from pop1: 86972
-> [readdata] lastread:86972 posi:14000031
-> Comparing positions: 1 with 0 has:253073
-> Only read nSites: 253073 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 83994
-> Sites to keep[12] from pop1: 83994
-> [readdata] lastread:83994 posi:14000031
-> Comparing positions: 1 with 0 has:337067
-> Only read nSites: 337067 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 79967
-> Sites to keep[16] from pop1: 79967
-> [readdata] lastread:79967 posi:14000031
-> Comparing positions: 1 with 0 has:417034
-> Only read nSites: 417034 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 72371
-> Sites to keep[17] from pop1: 72371
-> [readdata] lastread:72371 posi:14000031
-> Comparing positions: 1 with 0 has:489405
-> Only read nSites: 489405 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 76711
-> Sites to keep[18] from pop1: 76711
-> [readdata] lastread:76711 posi:14000031
-> Comparing positions: 1 with 0 has:566116
-> Only read nSites: 566116 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 69437
-> Sites to keep[19] from pop1: 69437
-> [readdata] lastread:69437 posi:14000031
-> Comparing positions: 1 with 0 has:635553
-> Only read nSites: 635553 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 70957
-> Sites to keep[2] from pop1: 70957
-> [readdata] lastread:70957 posi:14000031
-> Comparing positions: 1 with 0 has:706510
-> Only read nSites: 706510 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 77632
-> Sites to keep[20] from pop1: 77632
-> [readdata] lastread:77632 posi:14000031
-> Comparing positions: 1 with 0 has:784142
-> Only read nSites: 784142 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 72398
-> Sites to keep[3] from pop1: 72398
-> [readdata] lastread:72398 posi:14000031
-> Comparing positions: 1 with 0 has:856540
-> Only read nSites: 856540 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80535
-> Sites to keep[4] from pop1: 80535
-> [readdata] lastread:80535 posi:14000031
-> Comparing positions: 1 with 0 has:937075
-> Only read nSites: 937075 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 85060
-> Sites to keep[5] from pop1: 85060
-> [readdata] lastread:85060 posi:14000031
-> Comparing positions: 1 with 0 has:1022135
-> Only read nSites: 1022135 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 86081
-> Sites to keep[6] from pop1: 86081
-> [readdata] lastread:86081 posi:14000031
-> Comparing positions: 1 with 0 has:1108216
-> Only read nSites: 1108216 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 74829
-> Sites to keep[7] from pop1: 74829
-> [readdata] lastread:74829 posi:14000031
-> Comparing positions: 1 with 0 has:1183045
-> Only read nSites: 1183045 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 70120
-> Sites to keep[8] from pop1: 70120
-> [readdata] lastread:70120 posi:14000031
-> Comparing positions: 1 with 0 has:1253165
-> Only read nSites: 1253165 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 81441
-> Sites to keep[9] from pop1: 81441
-> [readdata] lastread:81441 posi:14000031
-> Comparing positions: 1 with 0 has:1334606
-> Only read nSites: 1334606 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1334606
------------
startlik=-2840247.303135
lik[2]=-186188.661577 diff=2.654059e+06 alpha:1.000000 sr2:5.368027e-01
lik[5]=-123469.414312 diff=6.271925e+04 alpha:1.325672 sr2:3.191128e-03
lik[8]=-123391.409082 diff=7.800523e+01 alpha:1.888191 sr2:3.966793e-08
lik[11]=-123338.315024 diff=5.309406e+01 alpha:4.000000 sr2:2.669970e-10
lik[14]=-123336.131056 diff=2.183968e+00 alpha:2.910030 sr2:2.128215e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):6.307042e-07
likelihood: -123336.131056
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447089 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1537126
-> The choice of -nSites will require atleast: 58.636703 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06985.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 82885
-> Sites to keep[1] from pop1: 82885
-> [readdata] lastread:82885 posi:14000031
-> Comparing positions: 1 with 0 has:82885
-> Only read nSites: 82885 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 86469
-> Sites to keep[10] from pop1: 86469
-> [readdata] lastread:86469 posi:14000031
-> Comparing positions: 1 with 0 has:169354
-> Only read nSites: 169354 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 87492
-> Sites to keep[11] from pop1: 87492
-> [readdata] lastread:87492 posi:14000031
-> Comparing positions: 1 with 0 has:256846
-> Only read nSites: 256846 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 83532
-> Sites to keep[12] from pop1: 83532
-> [readdata] lastread:83532 posi:14000031
-> Comparing positions: 1 with 0 has:340378
-> Only read nSites: 340378 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 82003
-> Sites to keep[16] from pop1: 82003
-> [readdata] lastread:82003 posi:14000031
-> Comparing positions: 1 with 0 has:422381
-> Only read nSites: 422381 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 68428
-> Sites to keep[17] from pop1: 68428
-> [readdata] lastread:68428 posi:14000031
-> Comparing positions: 1 with 0 has:490809
-> Only read nSites: 490809 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 76645
-> Sites to keep[18] from pop1: 76645
-> [readdata] lastread:76645 posi:14000031
-> Comparing positions: 1 with 0 has:567454
-> Only read nSites: 567454 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 80430
-> Sites to keep[19] from pop1: 80430
-> [readdata] lastread:80430 posi:14000031
-> Comparing positions: 1 with 0 has:647884
-> Only read nSites: 647884 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 67427
-> Sites to keep[2] from pop1: 67427
-> [readdata] lastread:67427 posi:14000031
-> Comparing positions: 1 with 0 has:715311
-> Only read nSites: 715311 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 75371
-> Sites to keep[20] from pop1: 75371
-> [readdata] lastread:75371 posi:14000031
-> Comparing positions: 1 with 0 has:790682
-> Only read nSites: 790682 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 72993
-> Sites to keep[3] from pop1: 72993
-> [readdata] lastread:72993 posi:14000031
-> Comparing positions: 1 with 0 has:863675
-> Only read nSites: 863675 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 80582
-> Sites to keep[4] from pop1: 80582
-> [readdata] lastread:80582 posi:14000031
-> Comparing positions: 1 with 0 has:944257
-> Only read nSites: 944257 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 86798
-> Sites to keep[5] from pop1: 86798
-> [readdata] lastread:86798 posi:14000031
-> Comparing positions: 1 with 0 has:1031055
-> Only read nSites: 1031055 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 87765
-> Sites to keep[6] from pop1: 87765
-> [readdata] lastread:87765 posi:14000031
-> Comparing positions: 1 with 0 has:1118820
-> Only read nSites: 1118820 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 72054
-> Sites to keep[7] from pop1: 72054
-> [readdata] lastread:72054 posi:14000031
-> Comparing positions: 1 with 0 has:1190874
-> Only read nSites: 1190874 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 67990
-> Sites to keep[8] from pop1: 67990
-> [readdata] lastread:67990 posi:14000031
-> Comparing positions: 1 with 0 has:1258864
-> Only read nSites: 1258864 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 78822
-> Sites to keep[9] from pop1: 78822
-> [readdata] lastread:78822 posi:14000031
-> Comparing positions: 1 with 0 has:1337686
-> Only read nSites: 1337686 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1337686
------------
startlik=-3408901.995403
lik[2]=-251790.013194 diff=3.157112e+06 alpha:1.000000 sr2:3.617810e-01
lik[5]=-121554.938267 diff=1.302351e+05 alpha:1.304712 sr2:1.309130e-02
lik[8]=-121415.189262 diff=1.397490e+02 alpha:1.752661 sr2:5.388610e-08
lik[11]=-121340.620216 diff=7.456905e+01 alpha:3.531047 sr2:6.657132e-10
lik[14]=-121339.499982 diff=1.120235e+00 alpha:1.813029 sr2:1.716519e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):6.796528e-07
likelihood: -121339.499982
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA06985.saf.idx is:2
-> Assuming .saf.gz file: smallNA06985.saf.gz
-> Assuming .saf.pos.gz: smallNA06985.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447091 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA06985.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 84197
-> Sites to keep[1] from pop1: 84197
-> [readdata] lastread:84197 posi:14000031
-> Comparing positions: 1 with 0 has:84197
-> Only read nSites: 84197 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 87278
-> Sites to keep[10] from pop1: 87278
-> [readdata] lastread:87278 posi:14000031
-> Comparing positions: 1 with 0 has:171475
-> Only read nSites: 171475 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 88240
-> Sites to keep[11] from pop1: 88240
-> [readdata] lastread:88240 posi:14000031
-> Comparing positions: 1 with 0 has:259715
-> Only read nSites: 259715 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 85784
-> Sites to keep[12] from pop1: 85784
-> [readdata] lastread:85784 posi:14000031
-> Comparing positions: 1 with 0 has:345499
-> Only read nSites: 345499 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 83373
-> Sites to keep[16] from pop1: 83373
-> [readdata] lastread:83373 posi:14000031
-> Comparing positions: 1 with 0 has:428872
-> Only read nSites: 428872 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 72661
-> Sites to keep[17] from pop1: 72661
-> [readdata] lastread:72661 posi:14000031
-> Comparing positions: 1 with 0 has:501533
-> Only read nSites: 501533 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 79369
-> Sites to keep[18] from pop1: 79369
-> [readdata] lastread:79369 posi:14000031
-> Comparing positions: 1 with 0 has:580902
-> Only read nSites: 580902 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 79063
-> Sites to keep[19] from pop1: 79063
-> [readdata] lastread:79063 posi:14000031
-> Comparing positions: 1 with 0 has:659965
-> Only read nSites: 659965 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 70800
-> Sites to keep[2] from pop1: 70800
-> [readdata] lastread:70800 posi:14000031
-> Comparing positions: 1 with 0 has:730765
-> Only read nSites: 730765 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 79048
-> Sites to keep[20] from pop1: 79048
-> [readdata] lastread:79048 posi:14000031
-> Comparing positions: 1 with 0 has:809813
-> Only read nSites: 809813 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 74298
-> Sites to keep[3] from pop1: 74298
-> [readdata] lastread:74298 posi:14000031
-> Comparing positions: 1 with 0 has:884111
-> Only read nSites: 884111 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 81743
-> Sites to keep[4] from pop1: 81743
-> [readdata] lastread:81743 posi:14000031
-> Comparing positions: 1 with 0 has:965854
-> Only read nSites: 965854 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 87910
-> Sites to keep[5] from pop1: 87910
-> [readdata] lastread:87910 posi:14000031
-> Comparing positions: 1 with 0 has:1053764
-> Only read nSites: 1053764 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 88960
-> Sites to keep[6] from pop1: 88960
-> [readdata] lastread:88960 posi:14000031
-> Comparing positions: 1 with 0 has:1142724
-> Only read nSites: 1142724 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 75973
-> Sites to keep[7] from pop1: 75973
-> [readdata] lastread:75973 posi:14000031
-> Comparing positions: 1 with 0 has:1218697
-> Only read nSites: 1218697 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 71302
-> Sites to keep[8] from pop1: 71302
-> [readdata] lastread:71302 posi:14000031
-> Comparing positions: 1 with 0 has:1289999
-> Only read nSites: 1289999 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 82849
-> Sites to keep[9] from pop1: 82849
-> [readdata] lastread:82849 posi:14000031
-> Comparing positions: 1 with 0 has:1372848
-> Only read nSites: 1372848 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1372848
------------
startlik=-2197168.603529
lik[2]=-143514.446220 diff=2.053654e+06 alpha:1.000000 sr2:5.974274e-01
lik[5]=-125724.416804 diff=1.779003e+04 alpha:1.332832 sr2:3.667813e-04
lik[8]=-125673.461579 diff=5.095522e+01 alpha:1.892596 sr2:1.467437e-08
lik[11]=-125638.522000 diff=3.493958e+01 alpha:3.911870 sr2:2.802106e-10
lik[14]=-125637.154132 diff=1.367868e+00 alpha:1.812501 sr2:1.170872e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):9.709660e-07
likelihood: -125637.154132
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447093 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11831.saf.idx):3
-> dim(smallNA11829.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 87760
-> Sites to keep[1] from pop1: 87760
-> [readdata] lastread:87760 posi:14000031
-> Comparing positions: 1 with 0 has:87760
-> Only read nSites: 87760 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 88140
-> Sites to keep[10] from pop1: 88140
-> [readdata] lastread:88140 posi:14000031
-> Comparing positions: 1 with 0 has:175900
-> Only read nSites: 175900 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 92014
-> Sites to keep[11] from pop1: 92014
-> [readdata] lastread:92014 posi:14000031
-> Comparing positions: 1 with 0 has:267914
-> Only read nSites: 267914 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 93575
-> Sites to keep[12] from pop1: 93575
-> [readdata] lastread:93575 posi:14000031
-> Comparing positions: 1 with 0 has:361489
-> Only read nSites: 361489 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 87923
-> Sites to keep[16] from pop1: 87923
-> [readdata] lastread:87923 posi:14000031
-> Comparing positions: 1 with 0 has:449412
-> Only read nSites: 449412 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 81332
-> Sites to keep[17] from pop1: 81332
-> [readdata] lastread:81332 posi:14000031
-> Comparing positions: 1 with 0 has:530744
-> Only read nSites: 530744 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 83694
-> Sites to keep[18] from pop1: 83694
-> [readdata] lastread:83694 posi:14000031
-> Comparing positions: 1 with 0 has:614438
-> Only read nSites: 614438 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 69471
-> Sites to keep[19] from pop1: 69471
-> [readdata] lastread:69471 posi:14000031
-> Comparing positions: 1 with 0 has:683909
-> Only read nSites: 683909 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 87051
-> Sites to keep[2] from pop1: 87051
-> [readdata] lastread:87051 posi:14000031
-> Comparing positions: 1 with 0 has:770960
-> Only read nSites: 770960 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 88957
-> Sites to keep[20] from pop1: 88957
-> [readdata] lastread:88957 posi:14000031
-> Comparing positions: 1 with 0 has:859917
-> Only read nSites: 859917 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 78004
-> Sites to keep[3] from pop1: 78004
-> [readdata] lastread:78004 posi:14000031
-> Comparing positions: 1 with 0 has:937921
-> Only read nSites: 937921 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 86910
-> Sites to keep[4] from pop1: 86910
-> [readdata] lastread:86910 posi:14000031
-> Comparing positions: 1 with 0 has:1024831
-> Only read nSites: 1024831 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 89735
-> Sites to keep[5] from pop1: 89735
-> [readdata] lastread:89735 posi:14000031
-> Comparing positions: 1 with 0 has:1114566
-> Only read nSites: 1114566 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 90378
-> Sites to keep[6] from pop1: 90378
-> [readdata] lastread:90378 posi:14000031
-> Comparing positions: 1 with 0 has:1204944
-> Only read nSites: 1204944 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 90285
-> Sites to keep[7] from pop1: 90285
-> [readdata] lastread:90285 posi:14000031
-> Comparing positions: 1 with 0 has:1295229
-> Only read nSites: 1295229 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 90409
-> Sites to keep[8] from pop1: 90409
-> [readdata] lastread:90409 posi:14000031
-> Comparing positions: 1 with 0 has:1385638
-> Only read nSites: 1385638 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 91714
-> Sites to keep[9] from pop1: 91714
-> [readdata] lastread:91714 posi:14000031
-> Comparing positions: 1 with 0 has:1477352
-> Only read nSites: 1477352 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1477352
------------
startlik=-2734619.025697
lik[2]=-168126.442971 diff=2.566493e+06 alpha:1.000000 sr2:5.929458e-01
lik[5]=-143873.512401 diff=2.425293e+04 alpha:1.246287 sr2:5.429294e-04
lik[8]=-143742.090681 diff=1.314217e+02 alpha:1.891768 sr2:2.596264e-08
lik[11]=-143734.499447 diff=7.591235e+00 alpha:3.355352 sr2:4.971104e-10
lik[14]=-143734.430854 diff=6.859282e-02 alpha:2.313781 sr2:8.056757e-12
-> Breaking EM(sr2) at iter:15, sqrt(sr2):1.002503e-07
likelihood: -143734.430854
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447095 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1556469
-> The choice of -nSites will require atleast: 59.374580 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11831.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 87418
-> Sites to keep[1] from pop1: 87418
-> [readdata] lastread:87418 posi:14000031
-> Comparing positions: 1 with 0 has:87418
-> Only read nSites: 87418 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 89825
-> Sites to keep[10] from pop1: 89825
-> [readdata] lastread:89825 posi:14000031
-> Comparing positions: 1 with 0 has:177243
-> Only read nSites: 177243 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 92238
-> Sites to keep[11] from pop1: 92238
-> [readdata] lastread:92238 posi:14000031
-> Comparing positions: 1 with 0 has:269481
-> Only read nSites: 269481 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 92422
-> Sites to keep[12] from pop1: 92422
-> [readdata] lastread:92422 posi:14000031
-> Comparing positions: 1 with 0 has:361903
-> Only read nSites: 361903 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 89345
-> Sites to keep[16] from pop1: 89345
-> [readdata] lastread:89345 posi:14000031
-> Comparing positions: 1 with 0 has:451248
-> Only read nSites: 451248 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 76772
-> Sites to keep[17] from pop1: 76772
-> [readdata] lastread:76772 posi:14000031
-> Comparing positions: 1 with 0 has:528020
-> Only read nSites: 528020 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 81896
-> Sites to keep[18] from pop1: 81896
-> [readdata] lastread:81896 posi:14000031
-> Comparing positions: 1 with 0 has:609916
-> Only read nSites: 609916 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 78597
-> Sites to keep[19] from pop1: 78597
-> [readdata] lastread:78597 posi:14000031
-> Comparing positions: 1 with 0 has:688513
-> Only read nSites: 688513 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 81941
-> Sites to keep[2] from pop1: 81941
-> [readdata] lastread:81941 posi:14000031
-> Comparing positions: 1 with 0 has:770454
-> Only read nSites: 770454 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 85672
-> Sites to keep[20] from pop1: 85672
-> [readdata] lastread:85672 posi:14000031
-> Comparing positions: 1 with 0 has:856126
-> Only read nSites: 856126 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 77237
-> Sites to keep[3] from pop1: 77237
-> [readdata] lastread:77237 posi:14000031
-> Comparing positions: 1 with 0 has:933363
-> Only read nSites: 933363 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 86266
-> Sites to keep[4] from pop1: 86266
-> [readdata] lastread:86266 posi:14000031
-> Comparing positions: 1 with 0 has:1019629
-> Only read nSites: 1019629 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 90693
-> Sites to keep[5] from pop1: 90693
-> [readdata] lastread:90693 posi:14000031
-> Comparing positions: 1 with 0 has:1110322
-> Only read nSites: 1110322 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 91624
-> Sites to keep[6] from pop1: 91624
-> [readdata] lastread:91624 posi:14000031
-> Comparing positions: 1 with 0 has:1201946
-> Only read nSites: 1201946 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 85747
-> Sites to keep[7] from pop1: 85747
-> [readdata] lastread:85747 posi:14000031
-> Comparing positions: 1 with 0 has:1287693
-> Only read nSites: 1287693 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 85832
-> Sites to keep[8] from pop1: 85832
-> [readdata] lastread:85832 posi:14000031
-> Comparing positions: 1 with 0 has:1373525
-> Only read nSites: 1373525 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 88011
-> Sites to keep[9] from pop1: 88011
-> [readdata] lastread:88011 posi:14000031
-> Comparing positions: 1 with 0 has:1461536
-> Only read nSites: 1461536 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1461536
------------
startlik=-3152181.517627
lik[2]=-194106.463861 diff=2.958075e+06 alpha:1.000000 sr2:5.288821e-01
lik[5]=-140190.841371 diff=5.391562e+04 alpha:1.226473 sr2:2.511108e-03
lik[8]=-140014.028145 diff=1.768132e+02 alpha:1.785354 sr2:3.928784e-08
lik[11]=-139985.591445 diff=2.843670e+01 alpha:4.000000 sr2:7.491422e-10
lik[14]=-139981.819412 diff=3.772034e+00 alpha:2.217838 sr2:3.742197e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):8.260068e-07
likelihood: -139981.819412
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11831.saf.idx is:2
-> Assuming .saf.gz file: smallNA11831.saf.gz
-> Assuming .saf.pos.gz: smallNA11831.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447098 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11831.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 89867
-> Sites to keep[1] from pop1: 89867
-> [readdata] lastread:89867 posi:14000031
-> Comparing positions: 1 with 0 has:89867
-> Only read nSites: 89867 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 91207
-> Sites to keep[10] from pop1: 91207
-> [readdata] lastread:91207 posi:14000031
-> Comparing positions: 1 with 0 has:181074
-> Only read nSites: 181074 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 93237
-> Sites to keep[11] from pop1: 93237
-> [readdata] lastread:93237 posi:14000031
-> Comparing positions: 1 with 0 has:274311
-> Only read nSites: 274311 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 95257
-> Sites to keep[12] from pop1: 95257
-> [readdata] lastread:95257 posi:14000031
-> Comparing positions: 1 with 0 has:369568
-> Only read nSites: 369568 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 90957
-> Sites to keep[16] from pop1: 90957
-> [readdata] lastread:90957 posi:14000031
-> Comparing positions: 1 with 0 has:460525
-> Only read nSites: 460525 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 81594
-> Sites to keep[17] from pop1: 81594
-> [readdata] lastread:81594 posi:14000031
-> Comparing positions: 1 with 0 has:542119
-> Only read nSites: 542119 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 85406
-> Sites to keep[18] from pop1: 85406
-> [readdata] lastread:85406 posi:14000031
-> Comparing positions: 1 with 0 has:627525
-> Only read nSites: 627525 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 77873
-> Sites to keep[19] from pop1: 77873
-> [readdata] lastread:77873 posi:14000031
-> Comparing positions: 1 with 0 has:705398
-> Only read nSites: 705398 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 86713
-> Sites to keep[2] from pop1: 86713
-> [readdata] lastread:86713 posi:14000031
-> Comparing positions: 1 with 0 has:792111
-> Only read nSites: 792111 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 90275
-> Sites to keep[20] from pop1: 90275
-> [readdata] lastread:90275 posi:14000031
-> Comparing positions: 1 with 0 has:882386
-> Only read nSites: 882386 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 79636
-> Sites to keep[3] from pop1: 79636
-> [readdata] lastread:79636 posi:14000031
-> Comparing positions: 1 with 0 has:962022
-> Only read nSites: 962022 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 88041
-> Sites to keep[4] from pop1: 88041
-> [readdata] lastread:88041 posi:14000031
-> Comparing positions: 1 with 0 has:1050063
-> Only read nSites: 1050063 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 92475
-> Sites to keep[5] from pop1: 92475
-> [readdata] lastread:92475 posi:14000031
-> Comparing positions: 1 with 0 has:1142538
-> Only read nSites: 1142538 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 92695
-> Sites to keep[6] from pop1: 92695
-> [readdata] lastread:92695 posi:14000031
-> Comparing positions: 1 with 0 has:1235233
-> Only read nSites: 1235233 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 91249
-> Sites to keep[7] from pop1: 91249
-> [readdata] lastread:91249 posi:14000031
-> Comparing positions: 1 with 0 has:1326482
-> Only read nSites: 1326482 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 90970
-> Sites to keep[8] from pop1: 90970
-> [readdata] lastread:90970 posi:14000031
-> Comparing positions: 1 with 0 has:1417452
-> Only read nSites: 1417452 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 93146
-> Sites to keep[9] from pop1: 93146
-> [readdata] lastread:93146 posi:14000031
-> Comparing positions: 1 with 0 has:1510598
-> Only read nSites: 1510598 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1510598
------------
startlik=-5402697.890442
lik[2]=-288910.933437 diff=5.113787e+06 alpha:1.000000 sr2:4.150039e-01
lik[5]=-145021.755650 diff=1.438892e+05 alpha:1.194627 sr2:1.609562e-02
lik[8]=-144871.646675 diff=1.501090e+02 alpha:1.626725 sr2:5.928644e-08
lik[11]=-144832.496077 diff=3.915060e+01 alpha:4.000000 sr2:6.468574e-10
lik[14]=-144824.257552 diff=8.238525e+00 alpha:2.131251 sr2:8.812961e-10
-> Breaking EM(sq2) at iter:16, sqrt(sq2):5.060953e-07
likelihood: -144824.257552
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447100 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1542786
-> The choice of -nSites will require atleast: 58.852615 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11829.saf.idx):3
-> dim(smallNA07056.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 86585
-> Sites to keep[1] from pop1: 86585
-> [readdata] lastread:86585 posi:14000031
-> Comparing positions: 1 with 0 has:86585
-> Only read nSites: 86585 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 88530
-> Sites to keep[10] from pop1: 88530
-> [readdata] lastread:88530 posi:14000031
-> Comparing positions: 1 with 0 has:175115
-> Only read nSites: 175115 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 92338
-> Sites to keep[11] from pop1: 92338
-> [readdata] lastread:92338 posi:14000031
-> Comparing positions: 1 with 0 has:267453
-> Only read nSites: 267453 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 90943
-> Sites to keep[12] from pop1: 90943
-> [readdata] lastread:90943 posi:14000031
-> Comparing positions: 1 with 0 has:358396
-> Only read nSites: 358396 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 87020
-> Sites to keep[16] from pop1: 87020
-> [readdata] lastread:87020 posi:14000031
-> Comparing positions: 1 with 0 has:445416
-> Only read nSites: 445416 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 76792
-> Sites to keep[17] from pop1: 76792
-> [readdata] lastread:76792 posi:14000031
-> Comparing positions: 1 with 0 has:522208
-> Only read nSites: 522208 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 81946
-> Sites to keep[18] from pop1: 81946
-> [readdata] lastread:81946 posi:14000031
-> Comparing positions: 1 with 0 has:604154
-> Only read nSites: 604154 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 74482
-> Sites to keep[19] from pop1: 74482
-> [readdata] lastread:74482 posi:14000031
-> Comparing positions: 1 with 0 has:678636
-> Only read nSites: 678636 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 82393
-> Sites to keep[2] from pop1: 82393
-> [readdata] lastread:82393 posi:14000031
-> Comparing positions: 1 with 0 has:761029
-> Only read nSites: 761029 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 84827
-> Sites to keep[20] from pop1: 84827
-> [readdata] lastread:84827 posi:14000031
-> Comparing positions: 1 with 0 has:845856
-> Only read nSites: 845856 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 77183
-> Sites to keep[3] from pop1: 77183
-> [readdata] lastread:77183 posi:14000031
-> Comparing positions: 1 with 0 has:923039
-> Only read nSites: 923039 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 86240
-> Sites to keep[4] from pop1: 86240
-> [readdata] lastread:86240 posi:14000031
-> Comparing positions: 1 with 0 has:1009279
-> Only read nSites: 1009279 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 89646
-> Sites to keep[5] from pop1: 89646
-> [readdata] lastread:89646 posi:14000031
-> Comparing positions: 1 with 0 has:1098925
-> Only read nSites: 1098925 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 90810
-> Sites to keep[6] from pop1: 90810
-> [readdata] lastread:90810 posi:14000031
-> Comparing positions: 1 with 0 has:1189735
-> Only read nSites: 1189735 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 85182
-> Sites to keep[7] from pop1: 85182
-> [readdata] lastread:85182 posi:14000031
-> Comparing positions: 1 with 0 has:1274917
-> Only read nSites: 1274917 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 84959
-> Sites to keep[8] from pop1: 84959
-> [readdata] lastread:84959 posi:14000031
-> Comparing positions: 1 with 0 has:1359876
-> Only read nSites: 1359876 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 87704
-> Sites to keep[9] from pop1: 87704
-> [readdata] lastread:87704 posi:14000031
-> Comparing positions: 1 with 0 has:1447580
-> Only read nSites: 1447580 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1447580
------------
startlik=-2093511.434168
lik[2]=-168207.705769 diff=1.925304e+06 alpha:1.000000 sr2:4.640896e-01
lik[5]=-139953.241695 diff=2.825446e+04 alpha:1.251799 sr2:7.411659e-04
lik[8]=-139797.816316 diff=1.554254e+02 alpha:1.913791 sr2:3.547014e-08
lik[11]=-139790.936605 diff=6.879711e+00 alpha:3.087171 sr2:6.136259e-10
-> Breaking EM(sq2) at iter:13, sqrt(sq2):7.303596e-07
likelihood: -139790.936605
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA11829.saf.idx is:2
-> Assuming .saf.gz file: smallNA11829.saf.gz
-> Assuming .saf.pos.gz: smallNA11829.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447103 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA11829.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 89033
-> Sites to keep[1] from pop1: 89033
-> [readdata] lastread:89033 posi:14000031
-> Comparing positions: 1 with 0 has:89033
-> Only read nSites: 89033 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 89820
-> Sites to keep[10] from pop1: 89820
-> [readdata] lastread:89820 posi:14000031
-> Comparing positions: 1 with 0 has:178853
-> Only read nSites: 178853 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 93406
-> Sites to keep[11] from pop1: 93406
-> [readdata] lastread:93406 posi:14000031
-> Comparing positions: 1 with 0 has:272259
-> Only read nSites: 272259 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 93847
-> Sites to keep[12] from pop1: 93847
-> [readdata] lastread:93847 posi:14000031
-> Comparing positions: 1 with 0 has:366106
-> Only read nSites: 366106 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 88713
-> Sites to keep[16] from pop1: 88713
-> [readdata] lastread:88713 posi:14000031
-> Comparing positions: 1 with 0 has:454819
-> Only read nSites: 454819 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 81915
-> Sites to keep[17] from pop1: 81915
-> [readdata] lastread:81915 posi:14000031
-> Comparing positions: 1 with 0 has:536734
-> Only read nSites: 536734 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 85416
-> Sites to keep[18] from pop1: 85416
-> [readdata] lastread:85416 posi:14000031
-> Comparing positions: 1 with 0 has:622150
-> Only read nSites: 622150 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 74194
-> Sites to keep[19] from pop1: 74194
-> [readdata] lastread:74194 posi:14000031
-> Comparing positions: 1 with 0 has:696344
-> Only read nSites: 696344 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 87081
-> Sites to keep[2] from pop1: 87081
-> [readdata] lastread:87081 posi:14000031
-> Comparing positions: 1 with 0 has:783425
-> Only read nSites: 783425 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 89410
-> Sites to keep[20] from pop1: 89410
-> [readdata] lastread:89410 posi:14000031
-> Comparing positions: 1 with 0 has:872835
-> Only read nSites: 872835 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 79408
-> Sites to keep[3] from pop1: 79408
-> [readdata] lastread:79408 posi:14000031
-> Comparing positions: 1 with 0 has:952243
-> Only read nSites: 952243 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 87879
-> Sites to keep[4] from pop1: 87879
-> [readdata] lastread:87879 posi:14000031
-> Comparing positions: 1 with 0 has:1040122
-> Only read nSites: 1040122 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 91337
-> Sites to keep[5] from pop1: 91337
-> [readdata] lastread:91337 posi:14000031
-> Comparing positions: 1 with 0 has:1131459
-> Only read nSites: 1131459 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 92014
-> Sites to keep[6] from pop1: 92014
-> [readdata] lastread:92014 posi:14000031
-> Comparing positions: 1 with 0 has:1223473
-> Only read nSites: 1223473 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 90377
-> Sites to keep[7] from pop1: 90377
-> [readdata] lastread:90377 posi:14000031
-> Comparing positions: 1 with 0 has:1313850
-> Only read nSites: 1313850 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 90045
-> Sites to keep[8] from pop1: 90045
-> [readdata] lastread:90045 posi:14000031
-> Comparing positions: 1 with 0 has:1403895
-> Only read nSites: 1403895 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 92641
-> Sites to keep[9] from pop1: 92641
-> [readdata] lastread:92641 posi:14000031
-> Comparing positions: 1 with 0 has:1496536
-> Only read nSites: 1496536 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1496536
------------
startlik=-3464322.520428
lik[2]=-210817.496481 diff=3.253505e+06 alpha:1.000000 sr2:4.767664e-01
lik[5]=-145816.421857 diff=6.500107e+04 alpha:1.217360 sr2:3.192777e-03
lik[8]=-145663.687067 diff=1.527348e+02 alpha:1.642686 sr2:4.984111e-08
lik[11]=-145620.779354 diff=4.290771e+01 alpha:4.000000 sr2:1.491300e-09
lik[14]=-145616.236324 diff=4.543030e+00 alpha:2.246424 sr2:6.378143e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):8.277280e-07
likelihood: -145616.236324
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))
-> Version of fname:smallNA07056.saf.idx is:2
-> Assuming .saf.gz file: smallNA07056.saf.gz
-> Assuming .saf.pos.gz: smallNA07056.saf.pos.gz
-> Version of fname:smallNA11830.saf.idx is:2
-> Assuming .saf.gz file: smallNA11830.saf.gz
-> Assuming .saf.pos.gz: smallNA11830.saf.pos.gz
-> args: tole:0.000001 nthreads:4 maxiter:100 nsites:0 start:(null) chr:(null) start:-1 stop:-1 fstout:(null) oldout:0 seed:1558447105 bootstrap:0 whichFst:0 fold:0 ref:(null) anc:(null)
-> Multi SFS is 'still' under development. Please report strange behaviour
-> nSites: 1584541
-> The choice of -nSites will require atleast: 60.445442 megabyte memory, that is at least: 0.02% of total memory
-> dim(smallNA07056.saf.idx):3
-> dim(smallNA11830.saf.idx):3
-> Dimension of parameter space: 9
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:1
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[1] from pop0: 89012
-> Sites to keep[1] from pop1: 89012
-> [readdata] lastread:89012 posi:14000031
-> Comparing positions: 1 with 0 has:89012
-> Only read nSites: 89012 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:10
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[10] from pop0: 91721
-> Sites to keep[10] from pop1: 91721
-> [readdata] lastread:91721 posi:14000031
-> Comparing positions: 1 with 0 has:180733
-> Only read nSites: 180733 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:11
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[11] from pop0: 93581
-> Sites to keep[11] from pop1: 93581
-> [readdata] lastread:93581 posi:14000031
-> Comparing positions: 1 with 0 has:274314
-> Only read nSites: 274314 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:12
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[12] from pop0: 92955
-> Sites to keep[12] from pop1: 92955
-> [readdata] lastread:92955 posi:14000031
-> Comparing positions: 1 with 0 has:367269
-> Only read nSites: 367269 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:16
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[16] from pop0: 90613
-> Sites to keep[16] from pop1: 90613
-> [readdata] lastread:90613 posi:14000031
-> Comparing positions: 1 with 0 has:457882
-> Only read nSites: 457882 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:17
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[17] from pop0: 77498
-> Sites to keep[17] from pop1: 77498
-> [readdata] lastread:77498 posi:14000031
-> Comparing positions: 1 with 0 has:535380
-> Only read nSites: 535380 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:18
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[18] from pop0: 83971
-> Sites to keep[18] from pop1: 83971
-> [readdata] lastread:83971 posi:14000031
-> Comparing positions: 1 with 0 has:619351
-> Only read nSites: 619351 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:19
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[19] from pop0: 84759
-> Sites to keep[19] from pop1: 84759
-> [readdata] lastread:84759 posi:14000031
-> Comparing positions: 1 with 0 has:704110
-> Only read nSites: 704110 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:2
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[2] from pop0: 81976
-> Sites to keep[2] from pop1: 81976
-> [readdata] lastread:81976 posi:14000031
-> Comparing positions: 1 with 0 has:786086
-> Only read nSites: 786086 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:20
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[20] from pop0: 86282
-> Sites to keep[20] from pop1: 86282
-> [readdata] lastread:86282 posi:14000031
-> Comparing positions: 1 with 0 has:872368
-> Only read nSites: 872368 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:3
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[3] from pop0: 79296
-> Sites to keep[3] from pop1: 79296
-> [readdata] lastread:79296 posi:14000031
-> Comparing positions: 1 with 0 has:951664
-> Only read nSites: 951664 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:4
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[4] from pop0: 87505
-> Sites to keep[4] from pop1: 87505
-> [readdata] lastread:87505 posi:14000031
-> Comparing positions: 1 with 0 has:1039169
-> Only read nSites: 1039169 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:5
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[5] from pop0: 92539
-> Sites to keep[5] from pop1: 92539
-> [readdata] lastread:92539 posi:14000031
-> Comparing positions: 1 with 0 has:1131708
-> Only read nSites: 1131708 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:6
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[6] from pop0: 93690
-> Sites to keep[6] from pop1: 93690
-> [readdata] lastread:93690 posi:14000031
-> Comparing positions: 1 with 0 has:1225398
-> Only read nSites: 1225398 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:7
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[7] from pop0: 86088
-> Sites to keep[7] from pop1: 86088
-> [readdata] lastread:86088 posi:14000031
-> Comparing positions: 1 with 0 has:1311486
-> Only read nSites: 1311486 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:8
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[8] from pop0: 85909
-> Sites to keep[8] from pop1: 85909
-> [readdata] lastread:85909 posi:14000031
-> Comparing positions: 1 with 0 has:1397395
-> Only read nSites: 1397395 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Is in multi sfs, will now read data from chr:9
-> hello Im the master merge part of realSFS. and I'll now do a tripple bypass to find intersect
-> 1) Will set iter according to chooseChr and start and stop, and possibly using -sites
-> Sites to keep[9] from pop0: 89002
-> Sites to keep[9] from pop1: 89002
-> [readdata] lastread:89002 posi:14000031
-> Comparing positions: 1 with 0 has:1486397
-> Only read nSites: 1486397 will therefore prepare next chromosome (or exit)
-> Done reading data from chromosome will prepare next chromosome
-> Will run optimization on nSites: 1486397
------------
startlik=-3927644.873384
lik[2]=-298081.140764 diff=3.629564e+06 alpha:1.000000 sr2:2.702135e-01
lik[5]=-140843.137737 diff=1.572380e+05 alpha:1.209936 sr2:1.616967e-02
lik[8]=-140718.641788 diff=1.244959e+02 alpha:1.600975 sr2:6.815642e-08
lik[11]=-140673.834390 diff=4.480740e+01 alpha:3.784730 sr2:2.332272e-10
lik[14]=-140670.849561 diff=2.984829e+00 alpha:2.040973 sr2:1.752269e-10
-> Breaking EM(sr2) at iter:15, sqrt(sr2):4.947789e-07
likelihood: -140670.849561
------------
-> Done reading data from chromosome will prepare next chromosome
-> Only read nSites: 0 will therefore prepare next chromosome (or exit)
-> NB NB output is no longer log probs of the frequency spectrum!
-> Output is now simply the expected values!
-> You can convert to the old format simply with log(norm(x))