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usegalaxy.* common tools
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Bug: sub-commands in Stringtie jobs result in no ouput -- only at ORG #840

Open jennaj opened 2 weeks ago

jennaj commented 2 weeks ago

Testing history: https://usegalaxy.eu/u/jenj/h/imported-from-archive-test-stringtie-bug-at-org-only

Contains the same test job run at ORG (this bug) and EU (success). AU also has success. Not sure why these differ, maybe due to some custom config at ORG?

Green results, some outputs populated, some empty (the actual count files). Impacts all tool versions I've tested, including the most current toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.3+galaxy0

Example ORG

Job API ID | bbd44e69cb8906b5b1dc488c5743e548 (60570475)

stderr

/usr/local/bin/prepDE.py:72: SyntaxWarning: invalid escape sequence '\-'
  RE_COVERAGE=re.compile('cov "([\-\+\d\.]+)"')
/usr/local/bin/prepDE.py:75: SyntaxWarning: invalid escape sequence '\-'
  RE_GFILE=re.compile('\-G\s*(\S+)') #assume filepath without spaces..

command line

mkdir -p ./special_de_output/sample1/ &&   ln -s '/jetstream2/scratch/main/jobs/60570475/inputs/dataset_3ee82ad4-801e-49b2-bea3-fa54692f1554.dat' guide.gff &&  stringtie '/jetstream2/scratch/main/jobs/60570475/inputs/dataset_5fcddd6f-1ecb-44f6-ab19-44f1d7f1e8fd.dat'  -o '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_c21cf612-30b0-47f5-bd39-81e8e7574af2.dat' -p "${GALAXY_SLOTS:-1}"    -G guide.gff -e -b ./special_de_output/sample1/  -f '0.01' -m '200' -a '10' -j '1' -c '1' -g '50' -M '1.0'    && ln -s '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_c21cf612-30b0-47f5-bd39-81e8e7574af2.dat' ./special_de_output/sample1/output.gtf && TAB=$(printf '\t') && CR=$(printf '\r') && prepDE.py -i ./special_de_output/ -g gene_counts.csv -t transcript_counts.csv -l 75 > /dev/null  && sed -i.bak -e "s/,/${TAB}/g" -e "s/${CR}//g" gene_counts.csv transcript_counts.csv && head -n 1 gene_counts.csv | sed -e 's/sample1/alignment_bam/' > '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_29fbe21c-fe83-4516-80a3-a385641e23d1.dat' && head -n 1 transcript_counts.csv | sed -e 's/sample1/alignment_bam/' > '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_a9b5c9bb-e021-48fe-8664-f7ba95c2027d.dat' && tail -n +2 gene_counts.csv | sort -t"${TAB}" -k1,1 >> '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_29fbe21c-fe83-4516-80a3-a385641e23d1.dat' && tail -n +2 transcript_counts.csv | sort -t"${TAB}" -k1,1 >> '/jetstream2/scratch/main/jobs/60570475/outputs/dataset_a9b5c9bb-e021-48fe-8664-f7ba95c2027d.dat'

Report at https://help.galaxyproject.org/t/stringetie-generating-empty-transcript-and-gene-counts/12831/