%%bash
echo "TODAY'S DATE"
date
echo "------------"
echo ""
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "
hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh
TODAY'S DATE Tue Jan 16 10:06:29 PST 2018 ------------ Distributor ID: Ubuntu Description: Ubuntu 16.04.3 LTS Release: 16.04 Codename: xenial ------------ HOSTNAME: swoose ------------ Computer Specs: Architecture: x86_64 CPU op-mode(s): 32-bit, 64-bit Byte Order: Little Endian CPU(s): 24 On-line CPU(s) list: 0-23 Thread(s) per core: 2 Core(s) per socket: 6 Socket(s): 2 NUMA node(s): 1 Vendor ID: GenuineIntel CPU family: 6 Model: 44 Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz Stepping: 2 CPU MHz: 2925.818 BogoMIPS: 5851.96 Virtualization: VT-x L1d cache: 32K L1i cache: 32K L2 cache: 256K L3 cache: 12288K NUMA node0 CPU(s): 0-23 Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat ------------ Memory Specs total used free shared buff/cache available Mem: 70G 4.3G 60G 384M 5.5G 65G Swap: 4.7G 0B 4.7G
No LSB modules are available.
canu_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta"
canu_sjw_01="/mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta"
pbjelly_sjw_01="/mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta"
platanus_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa"
platanus_sb_02="/mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa"
racon_sjw_01="/mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta"
redundans_sb_01="/mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa"
redundans_sb_02="/mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa"
redundans_sjw_01="/mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa"
redundans_sjw_02="/mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa"
redundans_sjw_03="/mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa"
soap_bgi_01="/mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa"
!python /home/sam/software/quast-4.5/quast.py \
-t 24 \
$canu_sb_01 \
$canu_sjw_01 \
$pbjelly_sjw_01 \
$platanus_sb_01 \
$platanus_sb_02 \
$racon_sjw_01 \
$redundans_sb_01 \
$redundans_sb_02 \
$redundans_sjw_01 \
$redundans_sjw_02 \
$redundans_sjw_03 \
$soap_bgi_01
/home/sam/software/quast-4.5/quast.py -t 24 /mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta /mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa /mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa /mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa Version: 4.5, 15ca3b9 System information: OS: Linux-4.4.0-109-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2018-01-16 10:08:35 Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/quast.log CWD: /home/sam/gitrepos/LabDocs/jupyter_nbs/sam Main parameters: Threads: 24, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 WARNING: Can't draw plots: python-matplotlib is missing or corrupted. Contigs: Pre-processing... 1 /mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta ==> oly_pacbio_.contigs 2 /mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta ==> 20171018_oly_pacbio.contigs 3 /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta ==> jelly.out 4 /mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa ==> Oly_Illumina_Platanus_Assembly_Oly_Out__contig 5 /mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa ==> Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 6 /mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta ==> 20170918_oly_pacbio_racon1_consensus 7 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa ==> Oly_Redundans_Output_scaffolds.reduced 8 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa ==> Oly_Redundans_Output_Try_2_scaffolds.reduced 9 /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa ==> 20171005_redundans_scaffolds.reduced 10 /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa ==> 20171004_redundans_scaffolds.reduced 11 /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa ==> 20171024_docker_oly_redundans_01_scaffolds.reduced 12 /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa ==> Ostrea_lurida 2018-01-16 10:11:11 Running Basic statistics processor... Contig files: 1 oly_pacbio_.contigs 2 20171018_oly_pacbio.contigs 3 jelly.out 4 Oly_Illumina_Platanus_Assembly_Oly_Out__contig 5 Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 6 20170918_oly_pacbio_racon1_consensus 7 Oly_Redundans_Output_scaffolds.reduced 8 Oly_Redundans_Output_Try_2_scaffolds.reduced 9 20171005_redundans_scaffolds.reduced 10 20171004_redundans_scaffolds.reduced 11 20171024_docker_oly_redundans_01_scaffolds.reduced 12 Ostrea_lurida Calculating N50 and L50... 1 oly_pacbio_.contigs, N50 = 14117, L50 = 1230, Total length = 46288879, GC % = 36.45, # N's per 100 kbp = 0.00 2 20171018_oly_pacbio.contigs, N50 = 13157, L50 = 3329, Total length = 132146852, GC % = 36.40, # N's per 100 kbp = 0.00 3 jelly.out, N50 = 12433, L50 = 26241, Total length = 1180563613, GC % = 36.57, # N's per 100 kbp = 6580.58 4 Oly_Illumina_Platanus_Assembly_Oly_Out__contig, N50 = 684, L50 = 2, Total length = 2693, GC % = 46.05, # N's per 100 kbp = 0.00 5 Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig, N50 = 1245, L50 = 97869, Total length = 417951161, GC % = 35.70, # N's per 100 kbp = 0.00 6 20170918_oly_pacbio_racon1_consensus, N50 = 13763, L50 = 896, Total length = 33483762, GC % = 36.43, # N's per 100 kbp = 0.00 7 Oly_Redundans_Output_scaffolds.reduced, N50 = 682, L50 = 40, Total length = 85207, GC % = 36.24, # N's per 100 kbp = 17127.70 8 Oly_Redundans_Output_Try_2_scaffolds.reduced, N50 = 4175, L50 = 32022, Total length = 513841258, GC % = 35.90, # N's per 100 kbp = 1019.31 9 20171005_redundans_scaffolds.reduced, N50 = 16565, L50 = 452, Total length = 29292260, GC % = 36.39, # N's per 100 kbp = 918.03 10 20171004_redundans_scaffolds.reduced, N50 = 17679, L50 = 573, Total length = 40561504, GC % = 36.46, # N's per 100 kbp = 695.24 11 20171024_docker_oly_redundans_01_scaffolds.reduced, N50 = 16998, L50 = 1724, Total length = 111139362, GC % = 36.34, # N's per 100 kbp = 626.41 12 Ostrea_lurida, N50 = 4204, L50 = 43989, Total length = 697528655, GC % = 35.83, # N's per 100 kbp = 19149.50 Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2018-01-16 10:14:02 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 1: Creating Icarus viewers... Done 2018-01-16 10:14:56 RESULTS: Text versions of total report are saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/report.html Icarus (contig browser) is saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/icarus.html Log saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/quast.log Finished: 2018-01-16 10:14:57 Elapsed time: 0:06:21.404593 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST!
%%bash
cp -pR quast_results/results_2018_01_16_10_08_35/ /mnt/owl/Athaliana/quast_results/
cp: cannot create directory '/mnt/owl/Athaliana/quast_results/results_2018_01_16_10_08_35': Permission denied
sudo
to cp, so did that outside of notebook.¶%%bash
ls /mnt/owl/Athaliana/quast_results/results_2018_01_16_10_08_35/
basic_stats icarus.html icarus_viewers quast.log report.html report.tex report.tsv report.txt transposed_report.tex transposed_report.tsv transposed_report.txt
OK, so this all worked. However, text file output is difficult to view in Jupyter notebook. View it here: http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.txt
Use this link to view color-coded table of output:
http://owl.fish.washington.edu/Athaliana/quast_results/results_2018_01_16_10_08_35/report.html