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Carrion-lab / bacLIFE

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Error in rule antismash #19

Open margarett opened 5 hours ago

margarett commented 5 hours ago

I've seen the previous issue #15 but I can't fix my issue even with --j 1

I am running 5 files for analysis (I don't know what I'm actually analyzing, just helping a friend who has little clue about Linux and command line...) and I always get this error:

Activating conda environment: antismash_bacLIFE
[Thu Oct  3 21:39:36 2024]
Error in rule antismash:
    jobid: 24
    input: intermediate_files/annot/rn6390_X00005_O/Saureus_rn6390_X00005_O.gbk
    output: intermediate_files/antismash/Saureus_rn6390_X00005_O/Saureus_rn6390_X00005_O.gbk
    conda-env: antismash_bacLIFE
    shell:
        antismash --cb-general --cb-knownclusters --cb-subclusters --output-dir intermediate_files/antismash/Saureus_rn6390_X00005_O/ --asf --pfam2go --genefinding-tool prodigal --smcog-trees intermediate_files/annot/rn6390_X00005_O/Saureus_rn6390_X00005_O.gbk
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message

antismash is installed in environment antismash_bacLIFE and the folder "intermediate_files/antismash/Saureus_rn6390_X00005_O" is temporarily created (and removed after the error).

I am now trying to run a single file at a time. Also edited the Snakemake file to add --debug to the shell parameter.

margarett commented 3 hours ago

I ran all files one by one, and it all fails at the same point. Here is the log

Set cluster sensitivity to -s 1.000000
Set cluster mode SET COVER
Set cluster iterations to 1
intermediate_files/clustering/mmseqDB_clu.dbtype exists already!
RuleException:
CalledProcessError in file /home/bruno/bacLIFE/Snakefile, line 158:
Command 'set -euo pipefail;  mmseqs cluster intermediate_files/clustering/mmseqDB intermediate_files/clustering/mmseqDB_clu intermediate_files/clustering/mmseqDB_temp --min-seq-id 0.95 --cov-mode 0 -c 0.8' returned non-zero exit status 1.
[Thu Oct  3 23:58:31 2024]
Error in rule clustering:
    jobid: 0
    input: intermediate_files/combined_proteins/combined_proteins.fasta
    output: intermediate_files/clustering/binary_matrix.txt, intermediate_files/clustering/protein_cluster

Exiting because a job execution failed. Look above for error message
WorkflowError:
At least one job did not complete successfully.
[Thu Oct  3 23:58:31 2024]
Error in rule clustering:
    jobid: 6
    input: intermediate_files/combined_proteins/combined_proteins.fasta
    output: intermediate_files/clustering/binary_matrix.txt, intermediate_files/clustering/protein_cluster

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message