simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
104 stars 30 forks source link

error during virsorter2 run #85

Closed javadgh6 closed 3 years ago

javadgh6 commented 3 years ago

I face the following error any idea? Error in rule remove_partial_gene: jobid: 123 output: iter-0/pp-circular-flt.gff, iter-0/pp-circular-flt.faa conda-env: /home/*****/tools/virsorter2_database/conda_envs/da9264f7 shell:

    Log=/home/****(*/camel-data/camel-megahit-out/virsorter_out/virsorter2.8kb_out/log/iter-0/step1-pp/circular-remove-partial-gene-common.log
    if [ circular = "circular" ]; then
        python /home/*****tools/anaconda2/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/circular-remove-partial-gene.py iter-0/pp-circular.gff iter-0/pp-circular-flt.gff &> $Log || { echo "See error detail in $Log" | python /home/*****/tools/anaconda2/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }
        python /home/*****/tools/anaconda2/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/filter-seqs-by-gff.py iter-0/pp-circular-flt.gff iter-0/pp-circular.faa iter-0/pp-circular-flt.faa
    else
        (cd iter-0 && ln -s pp-circular.gff pp-circular-flt.gff)
        (cd iter-0 && ln -s pp-circular.faa pp-circular-flt.faa)
    fi

    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Exiting because a job execution failed. Look above for error message

An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting Issues can be raised at: https://github.com/jiarong/VirSorter2/issues

simroux commented 3 years ago

Hi,

This repo is for VriSorter1, please report VirSorter2 issues/bugs at https://github.com/jiarong/VirSorter2

Thanks, Simon