Bioinformatics Recipe Cookbook

Results generated by running the recipe.

Parameters used during the run:

  • Accession numbers:Fish marker accession numbers
Output Messages
Messages printed to the standard output stream:
Creating sequence ID to taxonomy ID map (step 1)...
Sequence ID to taxonomy ID map already present, skipping map creation.
Estimating required capacity (step 2)...
Estimated hash table requirement: 1016684 bytes
Capacity estimation complete. [0.101s]
Building database files (step 3)...
Hash table already present, skipping database file build.
Database construction complete. [Total: 0.105s]
Other Messages
Messages printed to the standard error stream:
+ set -uex
+ ACC=/export/www/biostar-central/export/media/projects/cookbook/data-275/Fish_marker_sequences
+ N=1000
+ L=100
+ mkdir -p input output code
+ FASTA=input/reference.fa
+ READS=input/reads.fq
+ TAXONOMY=input/taxonomy.txt
+ REPORT=output/kraken2-report.txt
+ OUTPUT=output/kraken2-output.txt
+ ACCURACY=output/kraken2-accuracy.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
+ xtract -pattern DocumentSummary -element Caption,TaxId,Title
+ esummary
++ shasum input/reference.fa
++ cut -c 1-8
+ SHA=cd28e448
+ DB=/home/www/tmp/cd28e448
+ mkdir -p /home/www/tmp/cd28e448
+ ln -sf /home/www/refs/kraken2/taxonomy /home/www/tmp/cd28e448
+ kraken2-build --add-to-library input/reference.fa --db /home/www/tmp/cd28e448
Masking low-complexity regions of new file... done.
Added "input/reference.fa" to library (/home/www/tmp/cd28e448)
+ kraken2-build --build --db /home/www/tmp/cd28e448
+ 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.
+ URL1=https://raw.githubusercontent.com/biostars/biocode/master/scripts/fasta/simulate.py
+ curl https://raw.githubusercontent.com/biostars/biocode/master/scripts/fasta/simulate.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  2369  100  2369    0     0  11280      0 --:--:-- --:--:-- --:--:-- 11280
+ python code/simulate.py --fname input/reference.fa --count 1000
+ kraken2 -db /home/www/tmp/cd28e448 input/reads.fq --report-zero-counts --report output/kraken2-report.txt
Loading database information... done.
61000 sequences (6.10 Mbp) processed in 0.259s (14108.2 Kseq/m, 1410.82 Mbp/m).
  60878 sequences classified (99.80%)
  122 sequences unclassified (0.20%)
+ 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  3027  100  3027    0     0  13513      0 --:--:-- --:--:-- --:--:-- 13513
+ python code/validate.py -f output/kraken2-output.txt -t input/taxonomy.txt -c 1000

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