RNA-Seq¶
Module 3- Comparing counts in libraries; Differential expression with goal of getting a nice plot. There are a few ways to go about this. Essentially you will be mapping reads to scaffold and counting (with a little statistics). I will outline a few ways to about this below.
HotLink A primary skillset for this module is making a plot of DEGs in R. A great tutorial can be carried out be simply downloading this zipped directory - http://eagle.fish.washington.edu/whale/fish546/DESeq.zip. Inside is a Lake Trout RNA-seq table, and commented out R script. All you have to do is run the commands.
TOC¶
In [ ]:
!sed
CLC¶
CLC is probably the easiest way to get a table with count data..
In [1]:
#video how-to run RNA-seq on CLC
from IPython.display import YouTubeVideo
YouTubeVideo('8q60pm8LrIc')
Out[1]:
Once you have RNA-seq files you can take a join, but it makes more sense to "Run an Experiment in CLC"
In [7]:
#exported from version 6 - tab delimne
!head -2 /Volumes/web/cnidarian/fish546_0lyMF
"Feature ID" "Experiment - Range (original values)" "Experiment - IQR (original values)" "Experiment - Difference (original values)" "Experiment - Fold Change (original values)" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Expression values" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Gene length" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Unique gene reads" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Total gene reads" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - RPKM" "Male - Means" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Expression values" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Gene length" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Unique gene reads" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Total gene reads" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - RPKM" "Female - Means" comp10002_c0_seq1 5 5 -5 -2.667 8 569 8 8 0.513 8 3 569 3 3 0.294 3
In [ ]:
!awk -F '\t' '{print $1,$9,$15}' </Volumes/web/cnidarian/fish546_0lyMF> /Volumes/web/cnidarian/fish546_0lyMF2
In [15]:
!head /Volumes/web/cnidarian/fish546_0lyMF2
"Feature ID" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Total gene reads" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Total gene reads" comp10002_c0_seq1 8 3 comp10005_c0_seq1 6 4 comp10007_c0_seq1 21431 4484 comp10008_c0_seq1 8360 4759 comp10009_c0_seq1 16064 8768 comp1000_c0_seq1 52 5 comp10010_c0_seq1 15 8 comp10012_c0_seq1 4 1 comp10013_c0_seq1 5 3
In [16]:
!sed 's/"Feature ID" "Male - filtered_106A_Male_Mix_TAGCTT_L004_R1 (paired) RNA-Seq - Total gene reads" "Female - filtered_106A_Female_Mix_GATCAG_L004_R1 (paired) RNA-Seq - Total gene reads"/Feature M F/g' </Volumes/web/cnidarian/fish546_0lyMF2> /Volumes/web/cnidarian/fish546_0lyMF3
#sed 's/abc/XYZ/g' <infile> outfile
In [17]:
!head /Volumes/web/cnidarian/fish546_0lyMF3
Feature M F comp10002_c0_seq1 8 3 comp10005_c0_seq1 6 4 comp10007_c0_seq1 21431 4484 comp10008_c0_seq1 8360 4759 comp10009_c0_seq1 16064 8768 comp1000_c0_seq1 52 5 comp10010_c0_seq1 15 8 comp10012_c0_seq1 4 1 comp10013_c0_seq1 5 3
Just xy plot?¶
In [20]:
from pandas import *
frank = read_table("/Volumes/web/cnidarian/fish546_0lyMF3", # name of the data file
sep=" ", # what character separates each column?
na_values=["", " "]) # what values should be considered "blank" values?
In [21]:
frank.tail()
Out[21]:
| Feature | M | F | |
|---|---|---|---|
| 110062 | comp9993_c0_seq2 | 42 | 32 |
| 110063 | comp9994_c0_seq1 | 6 | 2 |
| 110064 | comp9996_c0_seq1 | 3 | 1 |
| 110065 | comp9998_c0_seq1 | 10965 | 6158 |
| 110066 | comp99_c0_seq1 | 1 | 1 |
In [23]:
%pylab inline
Populating the interactive namespace from numpy and matplotlib
WARNING: pylab import has clobbered these variables: ['load', 'info', 'datetime', 'save', 'set_printoptions', 'unique'] `%pylab --no-import-all` prevents importing * from pylab and numpy
In [24]:
import matplotlib.pyplot as plt
import numpy as np
M = frank.M
F = frank.F
#plot the data
plt.plot(M, F, 'bo')
plt.show()
In [ ]:
In [25]:
plt.plot(F, M, 'gs')
Out[25]:
[<matplotlib.lines.Line2D at 0x1088db190>]
In [26]:
plt.scatter(M, F)
xlim(0, 2000); ylim(0, 2000)
Out[26]:
(0, 2000)
In [30]:
fig = plt.loglog(M, F, 'gs')
plt.xlabel('Male Expression', fontsize=20)
plt.ylabel('Female Expression', fontsize=20)
plt.axis([0, 1000000, 0, 1000000])
Out[30]:
[0, 1000000, 0, 1000000]
DESeq¶
In [30]:
%reload_ext rmagic
In [32]:
%R library( "DESeq" )
Loading required package: Biobase
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following object(s) are masked from ‘package:stats’:
xtabs
The following object(s) are masked from ‘package:base’:
anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
rownames, sapply, setdiff, table, tapply, union, unique
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: locfit
locfit 1.5-8 2012-04-25
In [33]:
%R CountData<- read.table("/Volumes/web/cnidarian/fish546_0lyMF3",row.names=1, header=TRUE,)
Out[33]:
array([[ 8, 6, 21431, ..., 3, 10965, 1],
[ 3, 4, 4484, ..., 1, 6158, 1]], dtype=int32)
In [34]:
%R summary(CountData)
Out[34]:
array(['Min. : 0.0 ', '1st Qu.: 3.0 ', 'Median : 13.0 ',
'Mean : 249.1 ', '3rd Qu.: 76.0 ', 'Max. :1863281.0 ',
'Min. : 0.0 ', '1st Qu.: 2.0 ', 'Median : 9.0 ',
'Mean : 162.7 ', '3rd Qu.: 51.0 ', 'Max. :1602661.0 '],
dtype='|S19')
In [35]:
# check that it is correct
%R head (CountData)
Out[35]:
array([[ 8, 6, 21431, 8360, 16064, 52],
[ 3, 4, 4484, 4759, 8768, 5]], dtype=int32)
In [36]:
# assign factors
%R Treatment <- factor( c("Male","Female") )
Out[36]:
array([2, 1], dtype=int32)
In [37]:
# create a new data set
%R cds <- newCountDataSet( CountData, Treatment )
Out[37]:
array(<rpy2.rinterface.SexpS4 - Python:0x10e869600 / R:0x114d17958>, dtype=object)
In [38]:
# Estimate effective library size
%R LibrarySize <- estimateSizeFactors( cds )
%R sizeFactors( LibrarySize )
Out[38]:
array([ 1.21854359, 0.82065181])
In [39]:
#estimate Dispersons without replication
%R Dispersons <- estimateDispersions( LibrarySize, method="blind", sharingMode="fit-only" )
Out[39]:
array(<rpy2.rinterface.SexpS4 - Python:0x10e8696d8 / R:0x115688ee0>, dtype=object)
In [40]:
# calculate differential gene expression
%R DE <- nbinomTest( Dispersons, "Male", "Female" )
Out[40]:
array([['comp10002_c0_seq1', 'comp10005_c0_seq1', 'comp10007_c0_seq1', ...,
'comp9996_c0_seq1', 'comp9998_c0_seq1', 'comp99_c0_seq1'],
['5.11042261413', '4.89904260332', '11525.6691667', ...,
'1.84024950582', '8251.11924876', '1.01959769917'],
['6.56521445319', '4.92391083989', '17587.3888683', ...,
'2.46195541994', '8998.4470599', '0.820651806648'],
...,
['-0.844721774522', '-0.0146467759644', '-1.68652526171', ...,
'-1.01464677596', '-0.262056314759', '0.570315724757'],
['0.885218680234', '1.0', '0.147533184865', ..., '0.987554518138',
'0.820202806666', '1.0'],
['1.0', '1.0', '1.0', ..., '1.0', '1.0', '1.0']],
dtype='|S19')
In [42]:
#check data
%R head (DE)
Out[42]:
array([['comp10002_c0_seq1', 'comp10005_c0_seq1', 'comp10007_c0_seq1',
'comp10008_c0_seq1', 'comp10009_c0_seq1', 'comp1000_c0_seq1'],
['5.11042261413', '4.89904260332', '11525.6691667', '6329.84902822',
'11933.570417', '24.3833059521'],
['6.56521445319', '4.92391083989', '17587.3888683', '6860.64910358',
'13182.950622', '42.6738939457'],
['3.65563077507', '4.87417436676', '5463.94946514', '5799.04895285',
'10684.1902119', '6.09271795845'],
['0.556818181818', '0.989898989899', '0.310674285197',
'0.845262432942', '0.810455149101', '0.142773892774'],
['-0.844721774522', '-0.0146467759644', '-1.68652526171',
'-0.242528763051', '-0.303195746233', '-2.8081958985'],
['0.885218680234', '1.0', '0.147533184865', '0.833689827989',
'0.792097629318', '0.159574074145'],
['1.0', '1.0', '1.0', '1.0', '1.0', '1.0']],
dtype='|S17')
In [13]:
%R test.func <- function(x) {x^2}
Out[13]:
array(<rpy2.rinterface.SexpClosure - Python:0x107469480 / R:0x10244f470>, dtype=object)
In [16]:
%R test.func(939399339)
Out[16]:
array([ 8.82471118e+17])
In [17]:
%R plot(1:10,1:10)
In [45]:
%%R plotDE <- function (DE)
plot(
DE$baseMean,DE$log2FoldChange,log="x", pch=20, cex=.3
)
--------------------------------------------------------------------------- RRuntimeError Traceback (most recent call last) <ipython-input-45-9f148f99388e> in <module>() ----> 1 get_ipython().run_cell_magic(u'R', u'plotDE <- function (DE)', u'plot(\nDE$baseMean,DE$log2FoldChange,log="x", pch=20, cex=.3\n)') /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_cell_magic(self, magic_name, line, cell) 2127 magic_arg_s = self.var_expand(line, stack_depth) 2128 with self.builtin_trap: -> 2129 result = fn(magic_arg_s, cell) 2130 return result 2131 /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k) 189 # but it's overkill for just that one bit of state. 190 def magic_deco(arg): --> 191 call = lambda f, *a, **k: f(*a, **k) 192 193 if callable(arg): /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) 575 576 tmpd = tempfile.mkdtemp() --> 577 self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) 578 579 text_output = '' /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/__init__.pyc in __call__(self, string) 238 def __call__(self, string): 239 p = rinterface.parse(string) --> 240 res = self.eval(p) 241 return res 242 /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs) 84 v = kwargs.pop(k) 85 kwargs[r_k] = v ---> 86 return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs) /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs) 33 for k, v in kwargs.iteritems(): 34 new_kwargs[k] = conversion.py2ri(v) ---> 35 res = super(Function, self).__call__(*new_args, **new_kwargs) 36 res = conversion.ri2py(res) 37 return res RRuntimeError: Error in png("/var/folders/28/07h2q2ms7nd609f1ft3mj1240000gn/T/tmpyjbUQB/Rplots%03d.png", : too many open devices
In [33]:
%R plotDE <- function(DE) {
%R plot(DE$baseMean,DE$log2FoldChange,log="x", pch=20, cex=.3)
%R }
--------------------------------------------------------------------------- RRuntimeError Traceback (most recent call last) <ipython-input-33-7dfee8f87d37> in <module>() ----> 1 get_ipython().magic(u'R plotDE <- function(DE) {') 2 get_ipython().magic(u'R plot(DE$baseMean,DE$log2FoldChange,log="x", pch=20, cex=.3)') 3 get_ipython().magic(u'R }') /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in magic(self, arg_s) 2170 magic_name, _, magic_arg_s = arg_s.partition(' ') 2171 magic_name = magic_name.lstrip(prefilter.ESC_MAGIC) -> 2172 return self.run_line_magic(magic_name, magic_arg_s) 2173 2174 #------------------------------------------------------------------------- /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/core/interactiveshell.pyc in run_line_magic(self, magic_name, line) 2091 kwargs['local_ns'] = sys._getframe(stack_depth).f_locals 2092 with self.builtin_trap: -> 2093 result = fn(*args,**kwargs) 2094 return result 2095 /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/core/magic.pyc in <lambda>(f, *a, **k) 189 # but it's overkill for just that one bit of state. 190 def magic_deco(arg): --> 191 call = lambda f, *a, **k: f(*a, **k) 192 193 if callable(arg): /Users/sr320/anaconda/lib/python2.7/site-packages/IPython/extensions/rmagic.pyc in R(self, line, cell, local_ns) 575 576 tmpd = tempfile.mkdtemp() --> 577 self.r('png("%s/Rplots%%03d.png",%s)' % (tmpd.replace('\\', '/'), png_args)) 578 579 text_output = '' /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/__init__.pyc in __call__(self, string) 238 def __call__(self, string): 239 p = rinterface.parse(string) --> 240 res = self.eval(p) 241 return res 242 /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs) 84 v = kwargs.pop(k) 85 kwargs[r_k] = v ---> 86 return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs) /Users/sr320/anaconda/lib/python2.7/site-packages/rpy2-2.3.8-py2.7-macosx-10.5-x86_64.egg/rpy2/robjects/functions.pyc in __call__(self, *args, **kwargs) 33 for k, v in kwargs.iteritems(): 34 new_kwargs[k] = conversion.py2ri(v) ---> 35 res = super(Function, self).__call__(*new_args, **new_kwargs) 36 res = conversion.ri2py(res) 37 return res RRuntimeError: Error in png("/var/folders/28/07h2q2ms7nd609f1ft3mj1240000gn/T/tmpo5lt_R/Rplots%03d.png", : too many open devices
In [45]:
#Write out
%R write.table(DE, "/Volumes/web/cnidarian/fish546_0lyMF_DElist", row.names = FALSE, sep="\t")
In [ ]:
In [117]:
from pandas import *
pls2 = read_table("/Users/sr320/Desktop/DE.txt", # name of the data file
sep=" ", # what character separates each column?
na_values=["NA","", " "]) # what values should be considered "blank" values?
In [119]:
pls2.tail()
Out[119]:
<class 'pandas.core.frame.DataFrame'> Int64Index: 5 entries, 9360 to 9364 Data columns (total 8 columns): id 5 non-null values baseMean 5 non-null values baseMeanA 5 non-null values baseMeanB 5 non-null values foldChange 5 non-null values log2FoldChange 5 non-null values pval 5 non-null values padj 5 non-null values dtypes: float64(5), object(3)
In [120]:
#import matplotlib.pyplot as plt
#import numpy as np
#plot log2 fold changes against base means
base = pls2.baseMean
log = pls2.log2FoldChange
#plot the data
plt.plot(base, log, 'bo')
plt.show()
In [130]:
fig = plt.semilogy(base, log, 'rs')
plt.xlabel('my label', fontsize=20)
plt.axis([0, 10000, 0.0001, 100])
Out[130]:
[0, 10000, 0.0001, 100]
In [131]:
fig = plt.loglog(base, log, 'rs')
plt.xlabel('my label', fontsize=20)
plt.axis([0, 10000, 0.0001, 100])
Out[131]:
[0, 10000, 0.0001, 100]
In [ ]:
%R plot(
%R DE$baseMean,
%R DE$log2FoldChange,
%R log="x", pch=20, cex=.3,
%R col = ifelse (DE$padj < .05, "red", "black"))
%R plotDE(DE)
IPlant¶
Running the Tuxedo Suite- Two Trocophore and Two Umbo stage larvae libraries were compared. Modelled after this tutorial http://www.iplantcollaborative.org/learning-center/discovery-environment/differential-expression-rna-seq-tuxedo-method
In [27]:
from IPython.display import IFrame
IFrame('http://www.iplantcollaborative.org/learning-center/discovery-environment/differential-expression-rna-seq-tuxedo-method', width=700, height=350)
Out[27]:
In [1]:
!ils
/iplant/home/sr320: filtered_400_NoIndex_L006_R1.fastq.gz Galaxy10-[Cut_on_data_7].tabular Gil_1.fq.gz Gil_2.fq.gz oyster.v9.fa oyster.v9.glean.final.rename.CDS.gff solid0078_20091105_BB3.fastq solid0078_20091105_DH3.fastq SPID_and_GO_number.tabular Transcriptome_module1_blastxout_CE_modified.txt Unknown_Transcriptome_31545_contigs.fa C- /iplant/home/sr320/AltSplice C- /iplant/home/sr320/analyses C- /iplant/home/sr320/bamout C- /iplant/home/sr320/BiGo_larvae C- /iplant/home/sr320/bisque_data C- /iplant/home/sr320/Black_Abalone C- /iplant/home/sr320/cacheServiceTempDir C- /iplant/home/sr320/ce C- /iplant/home/sr320/Cgigas_v9 C- /iplant/home/sr320/coge_data C- /iplant/home/sr320/fish546 C- /iplant/home/sr320/iplant_ws C- /iplant/home/sr320/OlympiaOyster C- /iplant/home/sr320/OlyO_PacBio C- /iplant/home/sr320/OlyO_SNPhunt C- /iplant/home/sr320/qdod C- /iplant/home/sr320/RNAseq_co_BS
In [3]:
!icd Cgigas_v9
In [4]:
!ipwd
/iplant/home/sr320/Cgigas_v9
In [5]:
!ils
/iplant/home/sr320/Cgigas_v9: BiGillRNA_GACTAAGA_1.fastq BiGillRNA_GACTAAGA_2.fastq BiGoRNA_GTGTCTAC_1.fastq BiGoRNA_GTGTCTAC_2.fastq Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa Crassostrea_gigas.GCA_000297895.1.21.gff3 Crassostrea_gigas.GCA_000297895.1.21.gtf oyster.v9.glean.final.rename.gff T1.fq.gz T2.fq.gz U1.fq.gz U2.fq.gz C- /iplant/home/sr320/Cgigas_v9/Cuffdiff2_analysis1-2014-02-06-10-06-21.400 C- /iplant/home/sr320/Cgigas_v9/Cufflinks2_analysis1-2014-02-06-07-11-47.565 C- /iplant/home/sr320/Cgigas_v9/Cuffmerge2_analysis1-2014-02-06-09-54-32.913 C- /iplant/home/sr320/Cgigas_v9/logs C- /iplant/home/sr320/Cgigas_v9/TopHat2-PE_BiGill_BiGo-2014-02-02-09-12-25.697 C- /iplant/home/sr320/Cgigas_v9/TopHat2-PE_BiGill_BiGo-2014-02-02-09-12-31.220 C- /iplant/home/sr320/Cgigas_v9/TopHat2-SE_analysis1-2014-02-05-16-28-28.598 C- /iplant/home/sr320/Cgigas_v9/Uncompress_files_with_gunzip_analysis1-2014-02-05-15-59-31.208
In [23]:
!iget -f -V -r TopHat2-SE_analysis1-2014-02-05-16-28-28.598 /Volumes/web/whale/fish546/iplant
NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=sr320 NOTICE: irodsZone=iplant NOTICE: created irodsHome=/iplant/home/sr320 NOTICE: created irodsCwd=/iplant/home/sr320 NOTICE: irodsCwd=/iplant/home/sr320/Cgigas_v9 D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598 : D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/bam : From server: NumThreads=16, addr:128.196.172.248, port:20095, cookie=1785312142 T1.bam 524.354 MB | 40.243 sec | 16 thr | 13.030 MB/s T1.bam.bai 1.514 MB | 1.044 sec | 0 thr | 1.449 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20195, cookie=493382347 T2.bam 561.110 MB | 53.398 sec | 16 thr | 10.508 MB/s T2.bam.bai 1.474 MB | 1.217 sec | 0 thr | 1.211 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20387, cookie=789239133 U1.bam 1085.350 MB | 112.228 sec | 16 thr | 9.671 MB/s U1.bam.bai 1.612 MB | 1.238 sec | 0 thr | 1.303 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20256, cookie=81450217 U2.bam 1016.442 MB | 136.988 sec | 16 thr | 7.420 MB/s U2.bam.bai 1.616 MB | 1.398 sec | 0 thr | 1.156 MB/s D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/logs : condor-0-input-0-stderr 0.000 MB | 0.222 sec | 0 thr | 0.000 MB/s condor-0-input-0-stdout 0.035 MB | 0.095 sec | 0 thr | 0.374 MB/s condor-0-input-1-stderr 0.000 MB | 0.080 sec | 0 thr | 0.000 MB/s condor-0-input-1-stdout 0.035 MB | 0.094 sec | 0 thr | 0.376 MB/s condor-0-input-2-stderr 0.000 MB | 0.085 sec | 0 thr | 0.000 MB/s condor-0-input-2-stdout 0.035 MB | 0.111 sec | 0 thr | 0.321 MB/s condor-0-input-3-stderr 0.000 MB | 0.095 sec | 0 thr | 0.000 MB/s condor-0-input-3-stdout 0.035 MB | 0.105 sec | 0 thr | 0.339 MB/s condor-0-input-4-stderr 0.000 MB | 0.084 sec | 0 thr | 0.000 MB/s condor-0-input-4-stdout 0.035 MB | 0.089 sec | 0 thr | 0.398 MB/s condor-0-input-5-stderr 0.000 MB | 0.086 sec | 0 thr | 0.000 MB/s condor-0-input-5-stdout 0.034 MB | 0.092 sec | 0 thr | 0.370 MB/s condor-stderr-0 0.026 MB | 0.088 sec | 0 thr | 0.302 MB/s condor-stdout-0 0.011 MB | 0.098 sec | 0 thr | 0.114 MB/s iplant.cmd 0.001 MB | 0.098 sec | 0 thr | 0.006 MB/s iplant.sh 0.005 MB | 0.087 sec | 0 thr | 0.060 MB/s output-last-stderr 0.000 MB | 0.088 sec | 0 thr | 0.000 MB/s output-last-stdout 6.236 MB | 2.514 sec | 0 thr | 2.481 MB/s script-condor-log 0.003 MB | 0.098 sec | 0 thr | 0.032 MB/s script-error.log 0.000 MB | 0.213 sec | 0 thr | 0.000 MB/s script-output.log 0.000 MB | 0.222 sec | 0 thr | 0.000 MB/s D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/T1_out : D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/T1_out/logs : bam_merge_um.log 0.000 MB | 0.095 sec | 0 thr | 0.002 MB/s bowtie_build.log 0.011 MB | 0.087 sec | 0 thr | 0.124 MB/s bowtie.left_kept_reads.lo 0.000 MB | 0.087 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.084 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.082 sec | 0 thr | 0.003 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.084 sec | 0 thr | 0.002 MB/s g2f.err 0.000 MB | 0.079 sec | 0 thr | 0.002 MB/s g2f.out 0.000 MB | 0.081 sec | 0 thr | 0.001 MB/s gtf_juncs.log 0.000 MB | 0.077 sec | 0 thr | 0.004 MB/s juncs_db.log 0.190 MB | 0.303 sec | 0 thr | 0.627 MB/s long_spanning_reads.segs. 0.106 MB | 0.149 sec | 0 thr | 0.712 MB/s m2g_left_kept_reads.err 0.001 MB | 0.104 sec | 0 thr | 0.008 MB/s m2g_left_kept_reads.out 0.000 MB | 0.083 sec | 0 thr | 0.002 MB/s prep_reads.log 0.000 MB | 0.084 sec | 0 thr | 0.003 MB/s reports.log 0.190 MB | 0.181 sec | 0 thr | 1.049 MB/s reports.merge_bam.log 0.000 MB | 0.109 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.083 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.084 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.083 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.085 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.096 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.089 sec | 0 thr | 0.000 MB/s run.log 0.013 MB | 0.082 sec | 0 thr | 0.154 MB/s segment_juncs.log 0.493 MB | 0.271 sec | 0 thr | 1.818 MB/s tophat.log 0.003 MB | 0.100 sec | 0 thr | 0.035 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20291, cookie=688945789 accepted_hits.bam 524.354 MB | 41.036 sec | 16 thr | 12.778 MB/s align_summary.txt 0.000 MB | 0.149 sec | 0 thr | 0.001 MB/s deletions.bed 0.002 MB | 0.149 sec | 0 thr | 0.017 MB/s insertions.bed 0.003 MB | 0.165 sec | 0 thr | 0.019 MB/s junctions.bed 7.478 MB | 3.221 sec | 0 thr | 2.321 MB/s prep_reads.info 0.000 MB | 0.183 sec | 0 thr | 0.000 MB/s From server: NumThreads=5, addr:128.196.172.248, port:20353, cookie=2048619364 unmapped.bam 159.029 MB | 18.098 sec | 5 thr | 8.787 MB/s D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/T2_out : D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/T2_out/logs : bam_merge_um.log 0.000 MB | 0.102 sec | 0 thr | 0.002 MB/s bowtie_build.log 0.011 MB | 0.152 sec | 0 thr | 0.075 MB/s bowtie.left_kept_reads.lo 0.000 MB | 0.084 sec | 0 thr | 0.003 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.130 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.099 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.093 sec | 0 thr | 0.002 MB/s g2f.err 0.000 MB | 0.087 sec | 0 thr | 0.002 MB/s g2f.out 0.000 MB | 0.083 sec | 0 thr | 0.001 MB/s gtf_juncs.log 0.000 MB | 0.094 sec | 0 thr | 0.003 MB/s juncs_db.log 0.190 MB | 0.294 sec | 0 thr | 0.646 MB/s long_spanning_reads.segs. 0.079 MB | 0.157 sec | 0 thr | 0.501 MB/s m2g_left_kept_reads.err 0.003 MB | 0.088 sec | 0 thr | 0.031 MB/s m2g_left_kept_reads.out 0.000 MB | 0.304 sec | 0 thr | 0.001 MB/s prep_reads.log 0.000 MB | 0.085 sec | 0 thr | 0.003 MB/s reports.log 0.190 MB | 0.249 sec | 0 thr | 0.763 MB/s reports.merge_bam.log 0.000 MB | 0.079 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.088 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.109 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.091 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.139 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.082 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.091 sec | 0 thr | 0.000 MB/s run.log 0.013 MB | 0.090 sec | 0 thr | 0.141 MB/s segment_juncs.log 0.484 MB | 0.316 sec | 0 thr | 1.535 MB/s tophat.log 0.003 MB | 0.100 sec | 0 thr | 0.035 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20166, cookie=582043986 accepted_hits.bam 561.110 MB | 35.878 sec | 16 thr | 15.639 MB/s align_summary.txt 0.000 MB | 0.121 sec | 0 thr | 0.002 MB/s deletions.bed 0.074 MB | 0.263 sec | 0 thr | 0.280 MB/s insertions.bed 0.018 MB | 0.103 sec | 0 thr | 0.178 MB/s junctions.bed 7.312 MB | 3.096 sec | 0 thr | 2.362 MB/s prep_reads.info 0.000 MB | 0.080 sec | 0 thr | 0.001 MB/s From server: NumThreads=4, addr:128.196.172.248, port:20378, cookie=711356739 unmapped.bam 100.407 MB | 14.381 sec | 4 thr | 6.982 MB/s D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/U1_out : D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/U1_out/logs : bam_merge_um.log 0.000 MB | 0.171 sec | 0 thr | 0.001 MB/s bowtie_build.log 0.012 MB | 0.128 sec | 0 thr | 0.092 MB/s bowtie.left_kept_reads.lo 0.000 MB | 0.094 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.093 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.087 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.089 sec | 0 thr | 0.002 MB/s g2f.err 0.000 MB | 0.098 sec | 0 thr | 0.002 MB/s g2f.out 0.000 MB | 0.088 sec | 0 thr | 0.001 MB/s gtf_juncs.log 0.000 MB | 0.083 sec | 0 thr | 0.003 MB/s juncs_db.log 0.190 MB | 0.334 sec | 0 thr | 0.569 MB/s long_spanning_reads.segs. 0.116 MB | 0.172 sec | 0 thr | 0.676 MB/s m2g_left_kept_reads.err 0.004 MB | 0.083 sec | 0 thr | 0.045 MB/s m2g_left_kept_reads.out 0.000 MB | 0.094 sec | 0 thr | 0.002 MB/s prep_reads.log 0.000 MB | 0.207 sec | 0 thr | 0.001 MB/s reports.log 0.190 MB | 0.185 sec | 0 thr | 1.025 MB/s reports.merge_bam.log 0.000 MB | 0.091 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.087 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.089 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.090 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.090 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.090 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.094 sec | 0 thr | 0.000 MB/s run.log 0.013 MB | 0.096 sec | 0 thr | 0.133 MB/s segment_juncs.log 0.504 MB | 0.269 sec | 0 thr | 1.874 MB/s tophat.log 0.003 MB | 0.155 sec | 0 thr | 0.022 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20187, cookie=445338951 accepted_hits.bam 1085.350 MB | 148.014 sec | 16 thr | 7.333 MB/s align_summary.txt 0.000 MB | 0.182 sec | 0 thr | 0.001 MB/s deletions.bed 0.071 MB | 0.419 sec | 0 thr | 0.168 MB/s insertions.bed 0.030 MB | 0.140 sec | 0 thr | 0.211 MB/s junctions.bed 10.573 MB | 5.249 sec | 0 thr | 2.014 MB/s prep_reads.info 0.000 MB | 0.083 sec | 0 thr | 0.001 MB/s From server: NumThreads=7, addr:128.196.172.248, port:20398, cookie=869595600 unmapped.bam 217.499 MB | 21.016 sec | 7 thr | 10.349 MB/s D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/U2_out : D- /Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598/U2_out/logs : bam_merge_um.log 0.000 MB | 0.093 sec | 0 thr | 0.002 MB/s bowtie_build.log 0.011 MB | 0.156 sec | 0 thr | 0.072 MB/s bowtie.left_kept_reads.lo 0.000 MB | 0.087 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.083 sec | 0 thr | 0.003 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.084 sec | 0 thr | 0.002 MB/s bowtie.left_kept_reads.m2 0.000 MB | 0.110 sec | 0 thr | 0.002 MB/s g2f.err 0.000 MB | 0.080 sec | 0 thr | 0.002 MB/s g2f.out 0.000 MB | 0.134 sec | 0 thr | 0.000 MB/s gtf_juncs.log 0.000 MB | 0.073 sec | 0 thr | 0.004 MB/s juncs_db.log 0.190 MB | 0.330 sec | 0 thr | 0.575 MB/s long_spanning_reads.segs. 0.086 MB | 0.133 sec | 0 thr | 0.643 MB/s m2g_left_kept_reads.err 0.002 MB | 0.100 sec | 0 thr | 0.023 MB/s m2g_left_kept_reads.out 0.000 MB | 0.089 sec | 0 thr | 0.002 MB/s prep_reads.log 0.000 MB | 0.110 sec | 0 thr | 0.002 MB/s reports.log 0.190 MB | 0.189 sec | 0 thr | 1.005 MB/s reports.merge_bam.log 0.000 MB | 0.075 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.077 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.078 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.097 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.083 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.089 sec | 0 thr | 0.000 MB/s reports.samtools_sort.log 0.000 MB | 0.084 sec | 0 thr | 0.000 MB/s run.log 0.013 MB | 0.094 sec | 0 thr | 0.135 MB/s segment_juncs.log 0.505 MB | 0.421 sec | 0 thr | 1.201 MB/s tophat.log 0.003 MB | 0.093 sec | 0 thr | 0.037 MB/s From server: NumThreads=16, addr:128.196.172.248, port:20056, cookie=1573138072 accepted_hits.bam 1016.442 MB | 129.945 sec | 16 thr | 7.822 MB/s align_summary.txt 0.000 MB | 0.224 sec | 0 thr | 0.001 MB/s deletions.bed 0.049 MB | 0.215 sec | 0 thr | 0.226 MB/s insertions.bed 0.016 MB | 0.171 sec | 0 thr | 0.094 MB/s junctions.bed 10.519 MB | 4.404 sec | 0 thr | 2.389 MB/s prep_reads.info 0.000 MB | 0.079 sec | 0 thr | 0.001 MB/s From server: NumThreads=10, addr:128.196.172.248, port:20231, cookie=640055026 unmapped.bam 299.451 MB | 24.648 sec | 10 thr | 12.149 MB/s
In [24]:
!iget -f -V -r Cufflinks2_analysis1-2014-02-06-07-11-47.565 /Volumes/web/whale/fish546/iplant
NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=sr320 NOTICE: irodsZone=iplant NOTICE: created irodsHome=/iplant/home/sr320 NOTICE: created irodsCwd=/iplant/home/sr320 NOTICE: irodsCwd=/iplant/home/sr320/Cgigas_v9 D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565 : D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/gtf : From server: NumThreads=2, addr:128.196.172.248, port:20052, cookie=1212704161 T1_transcripts.gtf 35.832 MB | 7.305 sec | 2 thr | 4.905 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20283, cookie=180616609 T2_transcripts.gtf 33.549 MB | 6.560 sec | 2 thr | 5.114 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20212, cookie=809785660 U1_transcripts.gtf 51.636 MB | 9.592 sec | 2 thr | 5.383 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20354, cookie=776720173 U2_transcripts.gtf 51.753 MB | 9.405 sec | 2 thr | 5.503 MB/s D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/logs : condor-0-input-0-stderr 0.000 MB | 0.483 sec | 0 thr | 0.000 MB/s condor-0-input-0-stdout 0.034 MB | 0.743 sec | 0 thr | 0.046 MB/s condor-0-input-1-stderr 0.000 MB | 0.081 sec | 0 thr | 0.000 MB/s condor-0-input-1-stdout 0.034 MB | 0.128 sec | 0 thr | 0.268 MB/s condor-0-input-2-stderr 0.000 MB | 0.083 sec | 0 thr | 0.000 MB/s condor-0-input-2-stdout 0.035 MB | 0.127 sec | 0 thr | 0.272 MB/s condor-0-input-3-stderr 0.000 MB | 0.082 sec | 0 thr | 0.000 MB/s condor-0-input-3-stdout 0.035 MB | 0.246 sec | 0 thr | 0.140 MB/s From server: NumThreads=6, addr:128.196.172.248, port:20331, cookie=910006227 condor-stderr-0 178.741 MB | 20.473 sec | 6 thr | 8.730 MB/s condor-stdout-0 0.000 MB | 0.098 sec | 0 thr | 0.000 MB/s iplant.cmd 0.001 MB | 0.123 sec | 0 thr | 0.005 MB/s iplant.sh 0.004 MB | 0.140 sec | 0 thr | 0.028 MB/s output-last-stderr 0.000 MB | 0.135 sec | 0 thr | 0.000 MB/s output-last-stdout 1.257 MB | 0.808 sec | 0 thr | 1.555 MB/s script-condor-log 0.002 MB | 0.279 sec | 0 thr | 0.006 MB/s script-error.log 0.000 MB | 0.078 sec | 0 thr | 0.000 MB/s script-output.log 0.000 MB | 0.083 sec | 0 thr | 0.001 MB/s D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/T1_out : genes.fpkm_tracking 2.993 MB | 1.424 sec | 0 thr | 2.102 MB/s isoforms.fpkm_tracking 3.670 MB | 1.632 sec | 0 thr | 2.249 MB/s skipped.gtf 0.000 MB | 0.095 sec | 0 thr | 0.002 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20351, cookie=1911159344 transcripts.gtf 35.832 MB | 7.785 sec | 2 thr | 4.603 MB/s D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/T2_out : genes.fpkm_tracking 2.517 MB | 1.488 sec | 0 thr | 1.692 MB/s isoforms.fpkm_tracking 3.097 MB | 1.356 sec | 0 thr | 2.284 MB/s skipped.gtf 0.000 MB | 0.142 sec | 0 thr | 0.000 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20230, cookie=1418556777 transcripts.gtf 33.549 MB | 6.448 sec | 2 thr | 5.203 MB/s D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/U1_out : genes.fpkm_tracking 3.839 MB | 2.035 sec | 0 thr | 1.886 MB/s isoforms.fpkm_tracking 4.807 MB | 1.982 sec | 0 thr | 2.425 MB/s skipped.gtf 0.001 MB | 0.091 sec | 0 thr | 0.006 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20059, cookie=991686081 transcripts.gtf 51.636 MB | 9.319 sec | 2 thr | 5.541 MB/s D- /Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565/U2_out : genes.fpkm_tracking 3.987 MB | 2.132 sec | 0 thr | 1.870 MB/s isoforms.fpkm_tracking 4.969 MB | 2.130 sec | 0 thr | 2.333 MB/s skipped.gtf 0.000 MB | 0.093 sec | 0 thr | 0.002 MB/s From server: NumThreads=2, addr:128.196.172.248, port:20305, cookie=1058677661 transcripts.gtf 51.753 MB | 9.649 sec | 2 thr | 5.363 MB/s
In [25]:
!iget -f -V -r Cuffmerge2_analysis1-2014-02-06-09-54-32.913 /Volumes/web/whale/fish546/iplant
NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=sr320 NOTICE: irodsZone=iplant NOTICE: created irodsHome=/iplant/home/sr320 NOTICE: created irodsCwd=/iplant/home/sr320 NOTICE: irodsCwd=/iplant/home/sr320/Cgigas_v9 D- /Volumes/web/whale/fish546/iplant/Cuffmerge2_analysis1-2014-02-06-09-54-32.913 : D- /Volumes/web/whale/fish546/iplant/Cuffmerge2_analysis1-2014-02-06-09-54-32.913/cuffmerge_out : D- /Volumes/web/whale/fish546/iplant/Cuffmerge2_analysis1-2014-02-06-09-54-32.913/cuffmerge_out/logs : run.log 0.001 MB | 0.617 sec | 0 thr | 0.002 MB/s From server: NumThreads=4, addr:128.196.172.248, port:20254, cookie=1892227713 merged.gtf 104.946 MB | 11.997 sec | 4 thr | 8.748 MB/s From server: NumThreads=3, addr:128.196.172.248, port:20214, cookie=1985952212 merged_with_ref_ids.gtf 89.735 MB | 14.238 sec | 3 thr | 6.303 MB/s D- /Volumes/web/whale/fish546/iplant/Cuffmerge2_analysis1-2014-02-06-09-54-32.913/logs : condor-0-input-0-stderr 0.000 MB | 0.306 sec | 0 thr | 0.000 MB/s condor-0-input-0-stdout 0.035 MB | 0.250 sec | 0 thr | 0.141 MB/s condor-0-input-1-stderr 0.000 MB | 0.085 sec | 0 thr | 0.000 MB/s condor-0-input-1-stdout 0.035 MB | 0.146 sec | 0 thr | 0.242 MB/s condor-0-input-2-stderr 0.000 MB | 0.087 sec | 0 thr | 0.000 MB/s condor-0-input-2-stdout 0.035 MB | 0.191 sec | 0 thr | 0.185 MB/s condor-0-input-3-stderr 0.000 MB | 0.075 sec | 0 thr | 0.000 MB/s condor-0-input-3-stdout 0.035 MB | 0.106 sec | 0 thr | 0.332 MB/s condor-0-input-4-stderr 0.000 MB | 0.079 sec | 0 thr | 0.000 MB/s condor-0-input-4-stdout 0.034 MB | 0.093 sec | 0 thr | 0.368 MB/s condor-0-input-5-stderr 0.000 MB | 0.080 sec | 0 thr | 0.000 MB/s condor-0-input-5-stdout 0.035 MB | 0.083 sec | 0 thr | 0.427 MB/s condor-stderr-0 0.003 MB | 0.115 sec | 0 thr | 0.024 MB/s condor-stdout-0 0.000 MB | 0.078 sec | 0 thr | 0.000 MB/s iplant.cmd 0.001 MB | 0.081 sec | 0 thr | 0.008 MB/s iplant.sh 0.005 MB | 0.080 sec | 0 thr | 0.061 MB/s output-last-stderr 0.000 MB | 0.074 sec | 0 thr | 0.000 MB/s output-last-stdout 0.987 MB | 0.532 sec | 0 thr | 1.856 MB/s script-condor-log 0.001 MB | 0.164 sec | 0 thr | 0.007 MB/s script-error.log 0.000 MB | 0.076 sec | 0 thr | 0.000 MB/s script-output.log 0.000 MB | 0.081 sec | 0 thr | 0.001 MB/s Crassostrea_gigas.GCA_000 0.216 MB | 0.172 sec | 0 thr | 1.260 MB/s
In [26]:
!iget -f -V -r Cuffdiff2_analysis1-2014-02-06-10-06-21.400 /Volumes/web/whale/fish546/iplant
NOTICE: irodsHost=data.iplantcollaborative.org NOTICE: irodsPort=1247 NOTICE: irodsUserName=sr320 NOTICE: irodsZone=iplant NOTICE: created irodsHome=/iplant/home/sr320 NOTICE: created irodsCwd=/iplant/home/sr320 NOTICE: irodsCwd=/iplant/home/sr320/Cgigas_v9 D- /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400 : D- /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/cuffdiff_out : basic_plots.R 0.000 MB | 0.605 sec | 0 thr | 0.000 MB/s bias_params.info 0.000 MB | 0.149 sec | 0 thr | 0.000 MB/s cds.count_tracking 1.322 MB | 0.896 sec | 0 thr | 1.475 MB/s cds.diff 2.174 MB | 0.873 sec | 0 thr | 2.491 MB/s cds_exp.diff 2.732 MB | 1.227 sec | 0 thr | 2.227 MB/s cds.fpkm_tracking 2.856 MB | 1.225 sec | 0 thr | 2.330 MB/s cds.read_group_tracking 4.213 MB | 1.683 sec | 0 thr | 2.504 MB/s From server: NumThreads=3, addr:128.196.172.248, port:20372, cookie=1374012470 cuffData.db 93.927 MB | 12.684 sec | 3 thr | 7.405 MB/s gene_exp.diff 4.112 MB | 2.264 sec | 0 thr | 1.816 MB/s genes.count_tracking 2.037 MB | 1.028 sec | 0 thr | 1.981 MB/s genes.fpkm_tracking 4.516 MB | 1.886 sec | 0 thr | 2.395 MB/s genes.read_group_tracking 6.641 MB | 2.658 sec | 0 thr | 2.499 MB/s isoform_exp.diff 6.575 MB | 2.683 sec | 0 thr | 2.451 MB/s isoforms.count_tracking 3.393 MB | 1.490 sec | 0 thr | 2.277 MB/s isoforms.fpkm_tracking 7.012 MB | 2.997 sec | 0 thr | 2.340 MB/s isoforms.read_group_track 11.120 MB | 7.705 sec | 0 thr | 1.443 MB/s promoters.diff 2.885 MB | 2.147 sec | 0 thr | 1.344 MB/s read_groups.info 0.000 MB | 0.103 sec | 0 thr | 0.003 MB/s run.info 0.000 MB | 0.085 sec | 0 thr | 0.003 MB/s splicing.diff 4.130 MB | 2.844 sec | 0 thr | 1.452 MB/s tss_group_exp.diff 5.279 MB | 3.740 sec | 0 thr | 1.411 MB/s tss_groups.count_tracking 2.620 MB | 2.040 sec | 0 thr | 1.284 MB/s tss_groups.fpkm_tracking 5.406 MB | 3.736 sec | 0 thr | 1.447 MB/s tss_groups.read_group_tra 8.435 MB | 5.813 sec | 0 thr | 1.451 MB/s var_model.info 4.365 MB | 3.146 sec | 0 thr | 1.387 MB/s D- /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/graphs : density_plot.png 0.016 MB | 0.171 sec | 0 thr | 0.095 MB/s Troco_Umbo_scatter_plot.p 0.043 MB | 0.130 sec | 0 thr | 0.331 MB/s Troco_Umbo_volcano_plot.p 0.021 MB | 0.089 sec | 0 thr | 0.232 MB/s D- /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/logs : condor-0-input-0-stderr 0.000 MB | 0.161 sec | 0 thr | 0.000 MB/s condor-0-input-0-stdout 0.034 MB | 0.119 sec | 0 thr | 0.290 MB/s condor-0-input-1-stderr 0.000 MB | 0.089 sec | 0 thr | 0.000 MB/s condor-0-input-1-stdout 0.034 MB | 0.090 sec | 0 thr | 0.382 MB/s condor-0-input-2-stderr 0.000 MB | 0.088 sec | 0 thr | 0.000 MB/s condor-0-input-2-stdout 0.035 MB | 0.111 sec | 0 thr | 0.312 MB/s condor-0-input-3-stderr 0.000 MB | 0.086 sec | 0 thr | 0.000 MB/s condor-0-input-3-stdout 0.035 MB | 0.175 sec | 0 thr | 0.197 MB/s condor-0-input-4-stderr 0.000 MB | 0.087 sec | 0 thr | 0.000 MB/s condor-0-input-4-stdout 0.036 MB | 0.089 sec | 0 thr | 0.410 MB/s condor-stderr-0 0.003 MB | 0.089 sec | 0 thr | 0.032 MB/s condor-stdout-0 0.001 MB | 0.082 sec | 0 thr | 0.012 MB/s iplant.cmd 0.001 MB | 0.090 sec | 0 thr | 0.007 MB/s iplant.sh 0.004 MB | 0.102 sec | 0 thr | 0.041 MB/s output-last-stderr 0.000 MB | 0.084 sec | 0 thr | 0.000 MB/s output-last-stdout 1.599 MB | 1.225 sec | 0 thr | 1.305 MB/s script-condor-log 0.002 MB | 0.112 sec | 0 thr | 0.021 MB/s script-error.log 0.000 MB | 0.080 sec | 0 thr | 0.000 MB/s script-output.log 0.000 MB | 0.114 sec | 0 thr | 0.001 MB/s D- /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/sorted_data : genes.sorted_by_expressio 0.165 MB | 0.257 sec | 0 thr | 0.643 MB/s genes.sorted_by_expressio 1.015 MB | 0.833 sec | 0 thr | 1.218 MB/s genes.sorted_by_fold.sig. 0.165 MB | 0.213 sec | 0 thr | 0.774 MB/s genes.sorted_by_fold.txt 1.015 MB | 0.938 sec | 0 thr | 1.082 MB/s transcripts.sorted_by_exp 0.258 MB | 0.318 sec | 0 thr | 0.812 MB/s transcripts.sorted_by_exp 2.252 MB | 1.778 sec | 0 thr | 1.266 MB/s transcripts.sorted_by_fol 0.258 MB | 0.354 sec | 0 thr | 0.729 MB/s transcripts.sorted_by_fol 2.252 MB | 1.613 sec | 0 thr | 1.396 MB/s cuffdiff.stderr 2.543 MB | 1.863 sec | 0 thr | 1.365 MB/s From server: NumThreads=6, addr:128.196.172.248, port:20279, cookie=1191899484 rebuilt.gtf 179.009 MB | 33.993 sec | 6 thr | 5.266 MB/s
In [30]:
cd /Volumes/web/whale/fish546/iplant/
/Volumes/web/whale/fish546/iplant
In [33]:
ls
Cuffdiff2_analysis1-2014-02-06-10-06-21.400/ Cufflinks2_analysis1-2014-02-06-07-11-47.565/ Cuffmerge2_analysis1-2014-02-06-09-54-32.913/ TopHat2-SE_analysis1-2014-02-05-16-28-28.598/
In [34]:
cd TopHat2-SE_analysis1-2014-02-05-16-28-28.598/
/Volumes/web/whale/fish546/iplant/TopHat2-SE_analysis1-2014-02-05-16-28-28.598
In [35]:
ls
T1_out/ T2_out/ U1_out/ U2_out/ bam/ logs/
In [37]:
cd Cufflinks2_analysis1-2014-02-06-07-11-47.565/
/Volumes/web/whale/fish546/iplant/Cufflinks2_analysis1-2014-02-06-07-11-47.565
In [38]:
ls
T1_out/ T2_out/ U1_out/ U2_out/ gtf/ logs/
In [40]:
cd Cuffmerge2_analysis1-2014-02-06-09-54-32.913/
/Volumes/web/whale/fish546/iplant/Cuffmerge2_analysis1-2014-02-06-09-54-32.913
In [41]:
ls
Crassostrea_gigas.GCA_000297895.1.21.dna_rm.toplevel.fa.fai cuffmerge_out/ logs/
In [43]:
cd Cuffdiff2_analysis1-2014-02-06-10-06-21.400/
/Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400
In [44]:
ls
cuffdiff.stderr graphs/ rebuilt.gtf cuffdiff_out/ logs/ sorted_data/
In [45]:
cd graphs/
/Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/graphs
In [46]:
ls
Troco_Umbo_scatter_plot.png density_plot.png Troco_Umbo_volcano_plot.png
In [50]:
%pylab inline
Populating the interactive namespace from numpy and matplotlib
In [8]:
!sort -k8 -n /Volumes/web/whale/fish546/iplant/Cuffdiff2_analysis1-2014-02-06-10-06-21.400/sorted_data/genes.sorted_by_expression.sig.txt >/Volumes/web/cnidarian/fish546sort_gene.txt
In [13]:
!tail -100 /Volumes/web/cnidarian/fish546sort_gene.txt
EKC37475 CGI_10004362 Troco Umbo 14.84 UP 2.26 0.0453296 EKC39735 CGI_10018153 Troco Umbo 2.44 DOWN 20.77 0.0453296 XLOC_008830 - Troco Umbo 6.27 UP 12.18 0.0453296 XLOC_019776 - Troco Umbo 2.10 DOWN 73.97 0.0453296 XLOC_036014 - Troco Umbo 10.79 DOWN 3.87 0.0453296 EKC38006 CGI_10006955 Troco Umbo 3.40 DOWN 19.78 0.0455229 EKC39499 CGI_10027904 Troco Umbo 4.51 DOWN 3.57 0.0455229 XLOC_028766 - Troco Umbo 2.17 UP 89.68 0.0455229 EKC20773 CGI_10005392 Troco Umbo 3.65 UP 7.95 0.0457067 EKC30357 CGI_10021831 Troco Umbo 2.72 DOWN 53.16 0.0457067 XLOC_008243 - Troco Umbo 2.33 DOWN 47.08 0.0457067 EKC20007 CGI_10007068 Troco Umbo 21.26 UP 17.52 0.0458809 EKC22340 CGI_10002457 Troco Umbo 2.17 UP 19.26 0.0458809 XLOC_016380 - Troco Umbo 5.37 UP 23.55 0.0458809 XLOC_029734 - Troco Umbo 3.07 UP 169.21 0.0458809 XLOC_033553 - Troco Umbo 2.93 UP 305.69 0.0458809 EKC19008 CGI_10009987 Troco Umbo 4.07 DOWN 5.55 0.0460453 EKC28352 CGI_10011576 Troco Umbo 2.09 DOWN 102.97 0.0460453 EKC30991 CGI_10024990 Troco Umbo 2.69 DOWN 404.78 0.0460453 EKC36284 CGI_10010991 Troco Umbo 6.61 DOWN 1.57 0.0460453 EKC37698 CGI_10020451 Troco Umbo 5.62 DOWN 18.89 0.0460453 EKC28941 CGI_10016445 Troco Umbo 4.33 UP 4.63 0.0462281 EKC36463 CGI_10026996 Troco Umbo 3.58 UP 4.17 0.0462281 EKC39516 CGI_10027926 Troco Umbo 6.64 UP 14.89 0.0462281 XLOC_000090 - Troco Umbo 2.01 DOWN 3655.26 0.0462281 EKC24470 CGI_10019572 Troco Umbo 2.60 DOWN 7.05 0.0464106 XLOC_003648 - Troco Umbo 2.29 UP 58.71 0.0464106 XLOC_025872 - Troco Umbo 4.58 DOWN 7.88 0.0464106 XLOC_025928 CGI_10010307 Troco Umbo 3.12 DOWN 57.19 0.0464106 EKC23378 CGI_10012127 Troco Umbo 2.96 DOWN 244.69 0.0465834 EKC35004 CGI_10023624 Troco Umbo 13.31 UP 3.17 0.0465834 XLOC_000133 - Troco Umbo 5.34 DOWN 841.51 0.0465834 XLOC_004846 CGI_10004899 Troco Umbo 2.64 UP 8.34 0.0465834 XLOC_005195 - Troco Umbo 4.05 UP 42.18 0.0465834 XLOC_023099 - Troco Umbo 2.19 DOWN 90.02 0.0467936 EKC23538 CGI_10007959 Troco Umbo 2.09 DOWN 51.83 0.0469848 EKC40818 CGI_10026501 Troco Umbo 17.09 UP 3.20 0.0469848 XLOC_014332 - Troco Umbo 2.59 UP 14.38 0.0469848 EKC22776 CGI_10001495 Troco Umbo 64.30 DOWN 18.74 0.0471853 EKC24585 CGI_10024373 Troco Umbo 21.03 DOWN 13.52 0.0471853 EKC22688 CGI_10001711 Troco Umbo 10.52 UP 14.58 0.047376 EKC35331 CGI_10009319 Troco Umbo 8.81 DOWN 13.78 0.047376 EKC37827 CGI_10017650 Troco Umbo 3.03 DOWN 49.91 0.047376 EKC32649 CGI_10011464 Troco Umbo 13.03 UP 2.31 0.0475377 EKC40671 CGI_10014094 Troco Umbo 13.22 UP 2.50 0.0475377 EKC42689 CGI_10023910 Troco Umbo 13.66 UP 4.16 0.0475377 XLOC_001186 CGI_10000991 Troco Umbo 3.80 DOWN 95.81 0.0475377 XLOC_004854 - Troco Umbo 3.19 DOWN 494.38 0.0475377 XLOC_031373 - Troco Umbo 13.67 UP 6.56 0.0475377 EKC19599 CGI_10008154 Troco Umbo 2.77 DOWN 18.33 0.0477086 EKC20292 CGI_10006339 Troco Umbo 5391.68 UP 1.01 0.0477086 EKC24893 CGI_10021492 Troco Umbo 3.96 DOWN 7.22 0.0477086 EKC26706 CGI_10028240 Troco Umbo 4.54 UP 2.42 0.0477086 EKC34691 CGI_10026828 Troco Umbo 2.48 UP 14.28 0.0477086 EKC39440 CGI_10020043 Troco Umbo 2.65 UP 2.88 0.0479082 EKC39718 CGI_10018135 Troco Umbo 2.11 UP 43.18 0.0479082 EKC24748 CGI_10016919 Troco Umbo 2.56 DOWN 41.02 0.0480688 EKC31094 CGI_10028719 Troco Umbo 2.80 UP 94.15 0.0480688 EKC35815 CGI_10019085 Troco Umbo 5.28 DOWN 15.91 0.0480688 EKC38040 CGI_10007775 Troco Umbo 4.30 UP 2.77 0.0480688 EKC42277 CGI_10017847 Troco Umbo 4.09 UP 12.63 0.0480688 XLOC_010164 - Troco Umbo 2.15 DOWN 54.85 0.0480688 EKC17945 CGI_10000015 Troco Umbo 2.13 DOWN 450.32 0.0482194 EKC26388 CGI_10025849 Troco Umbo 1.98 DOWN 1418.81 0.0482194 EKC30309 CGI_10024543 Troco Umbo 5.79 UP 2.08 0.0482194 EKC31639 CGI_10009151 Troco Umbo 8.18 UP 3.93 0.0482194 EKC32392 CGI_10022269 Troco Umbo 3.80 UP 1.96 0.0482194 EKC36697 CGI_10010964 Troco Umbo 2.16 DOWN 38.89 0.0482194 EKC41655 CGI_10015739 Troco Umbo 2.83 DOWN 19.54 0.0482194 EKC19211 CGI_10009331 Troco Umbo 7.09 UP 3.80 0.0484084 XLOC_030085 CGI_10023149 Troco Umbo 2.18 DOWN 63.54 0.0484084 XLOC_034191 - Troco Umbo 15.88 DOWN 151.36 0.0484084 EKC23049 CGI_10000765 Troco Umbo 51.81 UP 3.02 0.0485777 EKC24201 CGI_10011140 Troco Umbo 16.59 UP 11.20 0.0485777 EKC38577 CGI_10025930 Troco Umbo 10.45 DOWN 3.83 0.0485777 XLOC_006086 - Troco Umbo 5.11 DOWN 311.86 0.0485777 XLOC_013300 CGI_10011136 Troco Umbo 9.23 UP 3.76 0.0485777 EKC42205 CGI_10028002 Troco Umbo 2.91 DOWN 20.39 0.0487857 EKC36733 CGI_10024965 Troco Umbo 2.74 UP 5.98 0.0489839 XLOC_006644 - Troco Umbo 10.24 DOWN 44.54 0.0489839 EKC27759 CGI_10015674 Troco Umbo 8.21 UP 2.12 0.049172 XLOC_014884 - Troco Umbo 6.49 UP 7.11 0.049172 EKC22964 CGI_10001026 Troco Umbo 110.46 UP 26.53 0.0493302 EKC23640 CGI_10009021 Troco Umbo 205.22 UP 48.28 0.0493302 EKC26438 CGI_10016881 Troco Umbo 140.92 UP 54.66 0.0493302 XLOC_011538 - Troco Umbo 19.76 DOWN 17404.94 0.0493302 XLOC_013596 - Troco Umbo 67.10 UP 97.19 0.0493302 EKC26111 CGI_10010243 Troco Umbo 2.10 DOWN 39.36 0.0495079 EKC29657 CGI_10026039 Troco Umbo 4.69 UP 24.15 0.0495079 EKC30968 CGI_10019769 Troco Umbo 2.62 DOWN 15.17 0.0495079 XLOC_015656 CGI_10028852 Troco Umbo 2.89 DOWN 34.63 0.0495079 EKC35109 CGI_10015126 Troco Umbo 2.21 UP 18.44 0.0496952 EKC35839 CGI_10019251 Troco Umbo 9.81 DOWN 2.33 0.0496952 XLOC_030804 CGI_10010458 Troco Umbo 5.40 UP 22.03 0.0496952 EKC18589 CGI_10011745 Troco Umbo 12.30 UP 2.92 0.0498525 EKC22366 CGI_10002407 Troco Umbo 1.98 DOWN 38.02 0.0498525 EKC26781 CGI_10013211 Troco Umbo 12.60 UP 22.29 0.0498525 EKC30487 CGI_10000421 Troco Umbo 2.80 DOWN 111.80 0.0498525 EKC31928 CGI_10012144 Troco Umbo 2.02 DOWN 30.63 0.0498525 XLOC_000878 - Troco Umbo 12.54 UP 7.81 0.0498525
In [21]:
!python /Users/sr320/sqlshare-pythonclient/tools/singleupload.py -d fish546_DEgene_out /Volumes/web/cnidarian/fish546sort_gene.txt
processing chunk line 0 to 2988 (0.50559592247 s elapsed) pushing /Volumes/web/cnidarian/fish546sort_gene.txt... parsing 25D12DC3... finished fish546_DEgene_out
In [23]:
cd /Volumes/web/cnidarian/
/Volumes/web/cnidarian
In [24]:
!python /Users/sr320/sqlshare-pythonclient/tools/fetchdata.py -s "SELECT * FROM [sr320@washington.edu].[fish546_DEgene_out]deg left join [sr320@washington.edu].[qDOD Cgigas Gene Descriptions (Swiss-prot)]sp on deg.gene_name = sp.CGI_ID" -f tsv -o fish546_DEGjoinSP.txt
In [25]:
!head fish546_DEGjoinSP.txt
In [28]:
!awk '{ print $10 }' fish546_DEGjoinSP.txt > fish546_DEGjoinSPonly.txt
In [30]:
!cat fish546_DEGjoinSPonly.txt
CGI_ID Q9BYW2 P47835 Q99NE9 P10817 Q5RF33 A7Y2W8 P84245 P23038 P47727 P37380 D2GXS7 P39963 Q91755 O70277 O61462 O75382 P49165 O35783 Q9ESN6 Q8WPJ2 Q8C525 Q801E2 O75382 O75382 P40631 Q6FY25 Q1HR24 Q60648 Q00341 P10039 P14543 Q7ZWG9 Q9CTN8 P54412 Q9ESN6 Q5BJP6 Q9VUL9 O75382 P24044 P61958 Q4GZT3 Q27245 A4IF63 O73792 Q8K0U4 Q8R431 Q5PQ71 Q717R8 Q9GJU1 B9A8D7 Q9BXJ4 P95896 Q8VI63 Q9JLF6 P50430 Q8R2Q0 Q09654 O42409 P70627 P08991 P18142 P61217 Q3UIW5 P57080 P10079 Q99758 A1L1W9 Q9BWU0 Q9QXE5 Q5HCP3 Q2MKA5 Q8WUD4 Q9EQW6 Q07837 Q90YC0 Q09654 Q9Y345 D2GXS7 Q9ESN6 P82003 O96064 P49242 Q9BY12 Q9Y3Q0 Q5UU75 Q61P40 Q6GLT8 P19623 O15460 P42765 P82198 Q5RBP9 Q92600 Q9WVR8 Q6PFY8 D3ZQG6 Q8BFR2 Q86XK2 D2GXS7 A0MGZ7 Q8K3P0 O77819 Q2KJA2 P08011 Q08830 P19477 A8K0R7 Q92038 A8Y1P7 P21439 Q9I9H2 Q92113 A4K526 P05790 Q920Q2 Q9ESN6 Q9Y6N5 P31430 Q9H307 P12394 Q9U943 Q0P5B7 Q9H204 C3YWU0 Q53T59 P53007 Q8TE56 Q8N413 Q8BID8 P62866 Q9CQ60 P19327 Q6TLH3 Q95WA4 P90893 P16157 P45961 A2RUS2 P51521 Q13247 O61462 Q90837 Q1T7C1 O95479 Q5E9K0 D2GXS7 P19827 Q9GZV8 Q9VCA2 Q5XKA2 B1WB06 Q8R151 Q3ZBH3 Q6AXS0 D2GXS7 P41827 P49011 Q13263 Q9H4A6 Q9R1K5 Q8MPM1 Q3U1V8 P34925 Q8BMZ5 Q63245 Q9NVA4 Q80X19 Q5SPB6 Q16534 Q3T0L7 Q9H477 Q5ZI03 P97414 Q15418 O14975 Q561R0 Q5BK43 O43301 P54513 P36956 O08623 Q20363 Q8R0S2 Q02357 Q4KTY1 O75382 Q5EGE1 Q8K1K9 O14522 A0JM12 A0JMK9 Q5TGI0 Q60648 Q562C7 P61594 Q2M1K9 Q7T3F7 P36954 Q09621 Q8N5R6 Q24423 Q566L4 P07686 O18373 Q4R3E0 Q0P5Y3 Q6PCJ1 Q460N5 P38650 Q9P2K9 Q174D3 Q99KH8 P04167 Q04786 P50429 Q0VA40 Q04861 Q8C8H8 O01666 Q8C8N3 Q29RI9 O70277 Q92051 P0C7B7 Q8WXK3 Q9Y0A7 Q9U3W6 O95208 Q6PFY8 Q9QYH9 O43557 P48067 Q5FW46 Q8JHV9 Q9QYE0 Q8R0S2 P23634 D2GXS7 P15800 P98164 Q9NWM8 Q9Z254 P50238 Q13490 P86789 Q8NHP8 Q0WR59 Q8IED2 Q14315 Q91W82 Q5U239 Q3USL1 Q64709 A7KAU2 Q6B966 D2GXS7 Q800H9 Q99MR0 Q9LQV2 Q96B67 O35261 P17439 A7RM45 Q92626 Q9H2H8 O75396 Q9EQD2 Q96MM6 Q9ESN6 O07552 Q24799 Q24799 Q503I8 Q95044 Q9IBG7 Q6VFT6 Q2TBT5 Q9CPY6 Q8VHS2 Q7ZYA2 C0H906 P50429 Q6DFQ5 Q9BXW9 P16924 P97524 Q8N695 Q8CJ12 Q5RBP9 Q28BT4 P77735 O75897 Q15397 Q5JTW2 Q07553 O17185 Q8JIR0 Q91648 P25386 P00639 O75581 P49165 Q9ESN6 O59922 Q7SXV2 O75382 Q2PZI1 Q96RW7 P39087 Q91755 O43301 P20742 Q9ERE8 P50416 Q96RW7 Q08CS6 Q05209 Q3KQ23 Q9NDE8 P24528 Q9ESN6 Q8BI84 Q8C8H8 Q8SWR2 Q9H299 Q8N0W4 Q8BNU0 Q05695 Q99735 Q9WYG0 Q8R0K9 Q969N2 P18163 P42664 P21775 P21775 Q9BXA5 Q60MF5 Q5RFE6 Q9VE46 P18172 P18503 P56533 Q63HN8 Q63HN8 O75901 Q9BG93 O14524 Q8BYF6 Q9ESN6 P24775 Q15428 Q80ZE5 Q50D79 Q9NFT7 C3YWU0 Q9PTU6 Q7ZVK3 Q61425 P29375 O75382 P10632 O11780 Q15582 O11780 Q9CZJ2 Q63425 P86956 Q01279 Q9BZW4 Q2QL79 O07552 Q863A5 Q5I2E5 A2TJ54 P16066 Q4TZY1 P30280 P49579 Q6WV74 P19374 P84051 P15870 P02299 P15870 A6NN14 P36633 O93430 Q9HC56 Q5M9G6 O88280 Q0II68 Q49YE0 Q65JE7 P98161 Q8IV36 Q28727 Q865F7 Q8N6F8 P32251 Q8BWF0 Q5RAL7 Q8VHW8 Q9Y2G4 Q61143 Q04164 O13008 Q504Y0 Q6ZRF8 Q9UL36 Q61140 P24862 Q6DDL7 P18700 O13085 Q0WYX8 Q15822 Q460N3 Q95JW3 Q0P5V2 Q1L8G7 Q96HJ9 Q54QQ2 Q8C827 Q8K199 Q5I7T1 Q52L14 Q9D554 G3V8T1 Q6NS23 Q8BHL8 Q54J55 Q9C040 O43172 Q2TBX6 A1A5Y0 P27447 Q54RV9 Q49LS8 A3KPN8 Q7Z5P4 P15308 P30050 Q8WU66 Q2M389 Q96P09 Q91Z53 Q8N2E2 Q6AYN4 Q6WYY1 P34269 Q92847 Q7Z6M2 Q5JXM2 Q8AXU4 Q9CQR6 O75382 Q9ESN6 P20965 Q62186 Q8R2E9 Q1LUS8 A2IBY8 Q92831 P22033 Q8MJD6 Q865K9 Q86WK9 Q40588 Q99P60 Q96JA1 O57590 Q54G96 O09131 Q6GLJ1 P97607 Q86Z23 Q9H1Q7 P49109 P53809 Q2EY13 Q1LYM3 P42325 P42325 Q86V71 Q96BD0 O05218 Q8WVM8 Q8N3Y7 P09487 P09487 P50133 Q4KL91 Q9Y284 Q5UR67 Q9NPJ3 Q9Y662 Q96IG2 P22897 P32870 Q5F415 Q09654 Q61627 Q6TL19 Q3MHN0 Q6GQ53 Q9JKP8 Q9ESN6 Q8C8H8 Q8C8H8 Q8C8H8 Q8C8H8 P46013 P43646 Q5R4Q3 P58751 Q9Y264 O95786 P82198 Q90YP3 Q6TFL4 Q8IZR5 O75382 A1L3F4 O60346 Q60FC1 Q9IAL1 Q8AYK6 Q8AVQ6 Q9VUL9 O93233 P34642 Q641K5 Q9DG68 Q9JIP0 P98063 Q6UWX4 P62277 Q8WVX9 Q9HBU6 Q3B8G0 P49869 P11046 Q3SZJ4 P18426 Q09654 A3KMV5 Q93098 P22488 Q923Z4 B2RUP2 O43614 Q5RAE3 Q59I64 Q8CEE6 Q80X19 Q9UET6 Q4VUF1 Q09225 E1BD59 P09848 P41996 Q07837 Q02241 Q7ZUP0 Q6FY25 Q6AYL5 A6YLM6 P33527 Q923L3 Q2M389 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