%%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 Nov 14 12:16:51 PST 2017
------------
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: 2925.853
BogoMIPS: 5851.97
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 tpr_shadow vnmi flexpriority ept vpid dtherm ida arat
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 4.8G 62G 236M 4.0G 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/20171114_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 /usr/local/bioinformatics/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
python: can't open file '/usr/local/bioinformatics/quast-4.5/quast.py': [Errno 2] No such file or directory
Whoops! Copy & paste error from a different notebook. Point to correct location of Quast on this computer...
!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/20171114_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-4.4.0-98-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64)
Python version: 2.7.12
CPUs number: 24
Started: 2017-11-14 12:30:25
Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2017_11_14_12_30_25/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/20171114_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
2017-11-14 12:32:54
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 = 4204, L50 = 43989, Total length = 697528655, GC % = 35.83, # N's per 100 kbp = 19162.18
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.
2017-11-14 12:35:17
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
1 of 1: Creating Icarus viewers...
Done
2017-11-14 12:36:03
RESULTS:
Text versions of total report are saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2017_11_14_12_30_25/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_2017_11_14_12_30_25/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_2017_11_14_12_30_25/report.html
Icarus (contig browser) is saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2017_11_14_12_30_25/icarus.html
Log saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2017_11_14_12_30_25/quast.log
Finished: 2017-11-14 12:36:04
Elapsed time: 0:05:38.666589
NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0
Thank you for using QUAST!
%%bash
cat quast_results/results_2017_11_14_12_30_25/report.txt
All statistics are based on contigs of size >= 500 bp, unless otherwise noted (e.g., "# contigs (>= 0 bp)" and "Total length (>= 0 bp)" include all contigs). Suggestion: assemblies jelly.out, Oly_Redundans_Output_scaffolds.reduced, Oly_Redundans_Output_Try_2_scaffolds.reduced, 20171005_redundans_scaffolds.reduced, 20171004_redundans_scaffolds.reduced, 20171024_docker_oly_redundans_01_scaffolds.reduced, Ostrea_lurida contain continuous fragments of N's of length >= 10 bp. You may consider rerunning QUAST using --scaffolds (-s) option! Assembly oly_pacbio_.contigs 20171018_oly_pacbio.contigs jelly.out Oly_Illumina_Platanus_Assembly_Oly_Out__contig Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 20170918_oly_pacbio_racon1_consensus Oly_Redundans_Output_scaffolds.reduced Oly_Redundans_Output_Try_2_scaffolds.reduced 20171005_redundans_scaffolds.reduced 20171004_redundans_scaffolds.reduced 20171024_docker_oly_redundans_01_scaffolds.reduced Ostrea_lurida # contigs (>= 0 bp) 3388 11246 765755 193390 12395459 2896 3642 300593 2078 2315 7408 765755 # contigs (>= 1000 bp) 3388 11246 184804 0 141851 2776 18 137301 1971 2315 7408 184804 # contigs (>= 5000 bp) 3338 10751 33792 0 2631 2492 0 24009 1744 2282 7270 33792 # contigs (>= 10000 bp) 2662 5469 8733 0 157 1715 0 6254 1202 1811 4127 8733 # contigs (>= 25000 bp) 119 547 553 0 0 88 0 586 204 304 823 553 # contigs (>= 50000 bp) 3 17 21 0 0 2 0 36 66 91 216 21 Total length (>= 0 bp) 46288879 132146852 776306190 16949361 1633553496 33496662 968128 546928670 29303793 40561504 111139362 776306190 Total length (>= 1000 bp) 46288879 132146852 642346712 0 257934533 33421961 25115 476206320 29235249 40561504 111139362 642346712 Total length (>= 5000 bp) 46112108 130500089 302087694 0 17549692 32715909 0 220366692 28679494 40443936 110651100 302087694 Total length (>= 10000 bp) 40284040 90550146 131223850 0 1977623 26428099 0 99646272 24316776 36412694 86479013 131223850 Total length (>= 25000 bp) 3651638 17592727 17851807 0 0 2808408 0 19574809 9732934 14794719 37385867 17851807 Total length (>= 50000 bp) 174603 940167 1283294 0 0 127712 0 2106424 5126002 7662042 17006058 1283294 # contigs 3388 11246 259186 4 373312 2856 114 188612 2045 2315 7408 259186 Largest contig 61184 76280 130073 764 23341 68522 3063 78788 252259 322397 256714 130073 Total length 46288879 132146852 697528655 2693 417951161 33483762 85207 513841258 29292260 40561504 111139362 697528655 GC (%) 36.45 36.40 35.83 46.05 35.70 36.43 36.24 35.90 36.39 36.46 36.34 35.83 N50 14117 13157 4204 684 1245 13763 682 4175 16565 17679 16998 4204 N75 11415 9066 2078 644 784 10543 569 2103 11605 12211 10536 2078 L50 1230 3329 43989 2 97869 896 40 32022 452 573 1724 43989 L75 2145 6369 103370 3 204757 1588 74 75613 984 1274 3823 103370 # N's per 100 kbp 0.00 0.00 19162.18 0.00 0.00 0.00 17127.70 1019.31 918.03 695.24 626.41 19149.50
%%bash
cp -pR quast_results/results_2017_11_14_12_30_25/ /mnt/owl/Athaliana/quast_results/
cp: cannot create directory '/mnt/owl/Athaliana/quast_results/results_2017_11_14_12_30_25': Permission denied
sudo to cp, so did that outside of notebook.¶%%bash
ls /mnt/owl/Athaliana/quast_results/results_2017_11_14_12_30_25/
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_2017_11_14_12_30_25/report.txt
Use this link to view color-coded table of output:
http://owl.fish.washington.edu/Athaliana/quast_results/results_2017_11_14_12_30_25/report.html