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shandley / hecatomb

hecatomb is a virome analysis pipeline for analysis of Illumina sequence data
MIT License
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Error in rule SECONDARY_AA_refactor_finalize #69

Closed Leran10 closed 1 year ago

Leran10 commented 2 years ago

Hi Michael,

I got error message on rule SECONDARY_AA_refactor_finalize:

Error in rule SECONDARY_AA_refactor_finalize:
    jobid: 2344
    output: hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/MMSEQS_AA_SECONDARY_lca.reformated
    log: hecatomb_out/STDERR/SECONDARY_AA_refactor_finalize.log (check log file(s) for error message)
    conda-env: /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/conda/8655527d2a89a42ca2366f81ff31244c
    shell:

        { cut -f1,2 hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/MMSEQS_AA_SECONDARY_lca.tsv             | taxonkit lineage --data-dir /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/tax/taxonomy -i 2             | taxonkit reformat --data-dir /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/tax/taxonomy -i 3                 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F --fill-miss-rank             | cut --complement -f3             > hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/MMSEQS_AA_SECONDARY_lca.reformated; } &> hecatomb_out/STDERR/SECONDARY_AA_refactor_finalize.log
        rm hecatomb_out/STDERR/SECONDARY_AA_refactor_finalize.log

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: Submitted batch job 36074265
Logfile hecatomb_out/STDERR/SECONDARY_AA_refactor_finalize.log not found.

Error executing rule SECONDARY_AA_refactor_finalize on cluster (jobid: 2344, external: Submitted batch job 36074265, jobscript: /scratch/sahlab/AK_V5/.snakemake/tmp.i459xfj8/snakejob.SECONDARY_AA_refactor_finalize.2344.sh). For error details see the cluster log and the log files of the involved rule(s).
Job failed, going on with independent jobs.

And same error in rule SECONDARY_AA_tophit_lineage:

Error in rule SECONDARY_AA_tophit_lineage:
    jobid: 2345
    output: hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/tophit.lineage.reformated
    log: hecatomb_out/STDERR/SECONDARY_AA_tophit_lineage.log (check log file(s) for error message)
    conda-env: /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/conda/8655527d2a89a42ca2366f81ff31244c
    shell:

        { # Make a table: SeqID <tab> taxID
        cut -f1,20 hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/MMSEQS_AA_SECONDARY_tophit_aln             | taxonkit lineage --data-dir /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/tax/taxonomy -i 2             | taxonkit reformat --data-dir /opt/apps/labs/sahlab/software/miniconda3/envs/hecatomb_v5/snakemake/workflow/../../databases/tax/taxonomy -i 3                 -f "{k}\t{p}\t{c}\t{o}\t{f}\t{g}\t{s}" -F --fill-miss-rank             | cut --complement -f3             > hecatomb_out/RESULTS/MMSEQS_AA_SECONDARY/tophit.lineage.reformated; } &> hecatomb_out/STDERR/SECONDARY_AA_tophit_lineage.log
        rm hecatomb_out/STDERR/SECONDARY_AA_tophit_lineage.log

        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
    cluster_jobid: Submitted batch job 36074266
Logfile hecatomb_out/STDERR/SECONDARY_AA_tophit_lineage.log not found.

Error executing rule SECONDARY_AA_tophit_lineage on cluster (jobid: 2345, external: Submitted batch job 36074266, jobscript: /scratch/sahlab/AK_V5/.snakemake/tmp.i459xfj8/snakejob.SECONDARY_AA_tophit_lineage.2345.sh). For error details see the cluster log and the log files of the involved rule(s).
Job failed, going on with independent jobs.
Exiting because a job execution failed. Look above for error message

    FATAL: Hecatomb encountered an error.
           Dumping all error logs to "hecatomb.errorLogs.txt"Complete log: /scratch/sahlab/AK_V5/.snakemake/log/2022-03-01T143143.794874.snakemake.log

I checked the log file hecatomb_out/STDERR/SECONDARY_AA_refactor_finalize.log and hecatomb_out/STDERR/SECONDARY_AA_tophit_lineage.log, they are empty.

Thanks! Leran

beardymcjohnface commented 2 years ago

Hi Leran, Were there any scheduler logs for this? e.g. logs/SECONDARY_AA_tophit_lineage/2345.err