+ 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