Job View: Results for Centrifuge classification validator: Fish marker accession numbers, 0.02

Results for Centrifuge classification validator: Fish marker accession numbers, 0.02

Results generated by running the recipe.

Completed

• Runtime 1 minutes • updated 3.8 years ago by Istvan Albert

Recipe Code Rerun Recipe Edit Result Delete Result

Results generated by running the recipe.

Parameters used during the run:

Accession numbers: Fish marker accession numbers
Error rates: 0.02

Files created by the recipe run:

accuracy-centrifuge.txt 6.2 KB

code/validate.py 3.9 KB

index/db.1.cf 8.3 MB

index/db.2.cf 98.9 KB

index/db.3.cf 8.5 KB

index/db.4.cf 744 bytes

input/accessions.txt 638 bytes

input/r1.fq 13.2 MB

input/r2.fq 13.2 MB

input/reference.fa 807.6 KB

input/taxonomy.txt 5.2 KB

log.txt 16 bytes

output/centrifuge-output.txt 5.6 MB

output/centrifuge-report.txt 14.4 KB

recipe.sh 3.0 KB

runlog.txt 5.8 KB

runlog/input.json 1.5 KB

runlog/stderr.txt 3.0 KB

runlog/stdout.txt 44 bytes

wgsim2/.git/HEAD 23 bytes

wgsim2/.git/config 272 bytes

wgsim2/.git/description 73 bytes

wgsim2/.git/hooks/applypatch-msg.sample 478 bytes

wgsim2/.git/hooks/commit-msg.sample 896 bytes

wgsim2/.git/hooks/post-update.sample 189 bytes

wgsim2/.git/hooks/pre-applypatch.sample 424 bytes

wgsim2/.git/hooks/pre-commit.sample 1.6 KB

wgsim2/.git/hooks/pre-push.sample 1.3 KB

wgsim2/.git/hooks/pre-rebase.sample 4.8 KB

wgsim2/.git/hooks/prepare-commit-msg.sample 1.2 KB

wgsim2/.git/hooks/update.sample 3.5 KB

wgsim2/.git/index 580 bytes

wgsim2/.git/info/exclude 240 bytes

wgsim2/.git/logs/HEAD 187 bytes

wgsim2/.git/logs/refs/heads/master 187 bytes

wgsim2/.git/logs/refs/remotes/origin/HEAD 187 bytes

wgsim2/.git/objects/19/c663057ef56dbdb4c612d8586a0d241821ae7b 16.8 KB

wgsim2/.git/objects/33/88c4cf9191c3eb5bd7e792dd103d30083574a3 244 bytes

wgsim2/.git/objects/34/5b5d9d0c1cc65710a504c79e1ef8f2dcefe107 2.6 KB

wgsim2/.git/objects/3e/336faf1afc22c3a45aadba411ab6d551d45930 47 bytes

wgsim2/.git/objects/5b/a985ee89b9c4c5ff31d6f4cee8f9f368dd419f 3.0 KB

wgsim2/.git/objects/72/fb86136762238e728818949b890b0f12d9aba9 54 bytes

wgsim2/.git/objects/cc/cf4564e4dda049870451f93addbd32eb003c67 555 bytes

wgsim2/.git/objects/dc/4aac2f31ce0aed30528fa460b7dcd0f0c4c211 215 bytes

wgsim2/.git/objects/e4/5d07b397d31aca2369a20eb367ce3671b08c76 59 bytes

wgsim2/.git/objects/f0/2b0954536119bfc9e80e2c104123c90f37e330 6.0 KB

wgsim2/.git/packed-refs 107 bytes

wgsim2/.git/refs/heads/master 41 bytes

wgsim2/.git/refs/remotes/origin/HEAD 32 bytes

wgsim2/.git/shallow 41 bytes

wgsim2/.gitignore 50 bytes

wgsim2/Makefile 409 bytes

wgsim2/README.md 6.2 KB

wgsim2/kseq.h 7.9 KB

wgsim2/log.txt 193 bytes

wgsim2/test/index/lambda.fa 48.1 KB

wgsim2/wgsim2 60.5 KB

wgsim2/wgsim2.c 17.1 KB

Messages printed to the standard output stream:

gcc -g -O2 -Wall -o wgsim2 wgsim2.c -lz -lm

Messages printed to the standard error stream:

+ ACC=/export/www/biostar-central/export/media/projects/cookbook/data-275/Fish_marker_sequences
+ TAXDIR=/home/www/refs/taxonomy
+ TABLE=/home/www/refs/taxonomy/table.txt
+ NODES=/home/www/refs/taxonomy/nodes.dmp
+ NAMES=/home/www/refs/taxonomy/names.dmp
+ mkdir -p /home/www/refs/taxonomy
+ N=1000
+ L=100
+ E=0.02
+ mkdir -p input output code
+ FASTA=input/reference.fa
+ R1=input/r1.fq
+ R2=input/r2.fq
+ TAXONOMY=input/taxonomy.txt
+ REPORT=output/centrifuge-report.txt
+ OUTPUT=output/centrifuge-output.txt
+ ACCURACY=accuracy-centrifuge.txt
+ cp /export/www/biostar-central/export/media/projects/cookbook/data-275/Fish_marker_sequences input/accessions.txt
+ epost -db nuccore -input /export/www/biostar-central/export/media/projects/cookbook/data-275/Fish_marker_sequences
+ efetch -format fasta
+ epost -db nuccore -input /export/www/biostar-central/export/media/projects/cookbook/data-275/Fish_marker_sequences
+ esummary
+ xtract -pattern DocumentSummary -element Caption,TaxId,Title
+ INDEX=index/db
+ mkdir -p index
+ centrifuge-build -p 2 --conversion-table /home/www/refs/taxonomy/table.txt --taxonomy-tree /home/www/refs/taxonomy/nodes.dmp --name-table /home/www/refs/taxonomy/names.dmp input/reference.fa index/db
+ pip install plac -q
WARNING: pip is being invoked by an old script wrapper. This will fail in a future version of pip.
Please see https://github.com/pypa/pip/issues/5599 for advice on fixing the underlying issue.
To avoid this problem you can invoke Python with '-m pip' instead of running pip directly.
+ git clone --depth=1 https://github.com/ialbert/wgsim2.git
Cloning into 'wgsim2'...
+ cd wgsim2
+ make
+ wgsim2/wgsim2 -f -r 0 -R 0 -N 1000 -e 0.02 -1 100 -2 100 input/reference.fa input/r1.fq input/r2.fq
[wgsim_core] skip sequence 'LC340162.1' as it is shorter than 650!
[wgsim_core] skip sequence 'LC340054.1' as it is shorter than 650!
[wgsim_core] skip sequence 'LC277930.1' as it is shorter than 650!
[wgsim_core] skip sequence 'KR476870.1' as it is shorter than 650!
+ centrifuge -x index/db -1 input/r1.fq -2 input/r2.fq -S output/centrifuge-output.txt --report-file output/centrifuge-report.txt
report file output/centrifuge-report.txt
Number of iterations in EM algorithm: 2
Probability diff. (P - P_prev) in the last iteration: 1.19883e-11
Calculating abundance: 00:00:00
+ centrifuge-kreport -x index/db output/centrifuge-output.txt
Loading taxonomy ...
Loading names file ...
Loading nodes file ...
+ URL2=https://raw.githubusercontent.com/biostars/biocode/master/scripts/classify/validate.py
+ curl https://raw.githubusercontent.com/biostars/biocode/master/scripts/classify/validate.py
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  3992  100  3992    0     0  20791      0 --:--:-- --:--:-- --:--:-- 20791
+ python code/validate.py -f output/centrifuge-output.txt -t input/taxonomy.txt -c 1000

Bioinformatics Recipe Cookbook