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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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classification Error? #4

Closed eawebb closed 4 years ago

eawebb commented 4 years ago

hi jiarong,

This new version looks really exciting (recommended to me by matt), and i have been able to run the test dataset to finish. i used the new conda install that you suggested in the other issue, plus the old one in the read me (adding conda screed). it is running on a centos HPC. it gets towards what i think is the end of the job when it is trying to collate the summary data files and crashes.

my command was: virsorter run -w vs2_results_7_25/st19.out -i /scratch/eawebb/rough_megahit_contigs/output_st19_final.contigs.fa --provirus-off --max-orf-per-seq 20 --min-length 700 --include-groups "dsDNAphage,ssDNA,RNA" -j 24

and the error log is below (this was the command that was calling up screed in my previous error).

[2020-07-25 15:49 INFO] conig file written to /scratch/eawebb/vs2_results_7_25/st19.out/config.yaml

[2020-07-25 15:49 INFO] Executing: snakemake --snakefile /scratch/eawebb/miniconda/envs/vs2/lib/python3.8/site-packages/virsorter/Snakefile --directory /scratch/eawebb/vs2_results_7_25/st19.out --jobs 24 --configfile /scratch/eawebb/vs2_results_7_25/st19.out/config.yaml --conda-prefix /scratch/eawebb/db/conda_envs --rerun-incomplete --use-conda --nolock --latency-wait 600 --quiet all Job counts: count jobs 1 all 1 classify 1 finalize 3 *** Usage: python add-suffix-seqname-keep-desc.py suffix /usr/bin/bash: full: command not found [Sat Jul 25 15:49:18 2020] Error in rule finalize: jobid: 8 output: final-viral-combined.fa, final-viral-score.tsv shell:

        python /scratch/eawebb/miniconda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/add-suffix-seqname-keep-desc.py iter-0/viral-fullseq.fa ||full > final-viral-combined.fa
        python /scratch/eawebb/miniconda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/add-suffix-seqname-keep-desc.py iter-0/viral-lt2gene-w-hallmark.fa ||lt2gene >> final-viral-combined.fa
        cp iter-0/all-fullseq-proba.tsv final-viral-score.tsv
        N_viral_fullseq=$(grep -c '^>' iter-0/viral-fullseq.fa || :)
        N_viral_lt2gene=$(grep -c '^>' iter-0/viral-lt2gene-w-hallmark.fa || :)
        echo -e "
        ====> VirSorter run (non-provirus mode) finished.
        # of viral contigs:   $N_viral_fullseq
        # of short viral contigs (<2 genes):  $N_viral_lt2gene

        Useful output files:
        final-viral-score.tsv
        final-viral-combined.fa
        <====
        " | python /scratch/eawebb/miniconda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/echo.py

    (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 [2020-07-25 15:49 CRITICAL] Command 'snakemake --snakefile /scratch/eawebb/miniconda/envs/vs2/lib/python3.8/site-packages/virsorter/Snakefile --directory /scratch/eawebb/vs2_results_7_25/st19.out --jobs 24 --configfile /scratch/eawebb/vs2_results_7_25/st19.out/config.yaml --conda-prefix /scratch/eawebb/db/conda_envs --rerun-incomplete --use-conda --nolock --latency-wait 600 --quiet all ' returned non-zero exit status 1.

Thanks eric

jiarong commented 4 years ago

fixed