issue during virsorter2 run

Hi there, I've recieved the follwing issue when running virsorter2 [2020-12-18 05:43 INFO] # of seqs < 1000 bp and removed: 0 [2020-12-18 05:43 INFO] # of circular seqs: 1294 [2020-12-18 05:43 INFO] # of linear seqs : 62424 [2020-12-18 05:43 INFO] Finish spliting circular contig file with common rbs [2020-12-18 05:43 INFO] Finish spliting linear contig file with common rbs [2020-12-18 05:45 INFO] Step 1 - preprocess finished. [2020-12-18 10:58 INFO] Step 2 - extract-feature finished. [2020-12-18 11:06 ERROR] See error details in /srv/projects/coral/Accelerate_project/analyses/20201002_viral_prep/20201218_VIRSorter2_RNA_viruses/iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.log [Fri Dec 18 11:06:44 2020] Error in rule provirus_call_by_group_by_split: jobid: 86 output: iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.bdy, iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.ftr conda-env: /srv/home/s4549287/db/conda_envs/cadc5396 shell:

        Log=/srv/projects/coral/Accelerate_project/analyses/20201002_viral_prep/20201218_VIRSorter2_RNA_viruses/iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.log
        Hallmark_list_f=/srv/home/s4549287/db/group/RNA/hallmark-gene.list
        if [ -s $Hallmark_list_f ]; then
            python /srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/provirus.py iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split iter-0/RNA/all.pdg.hmm.tax /srv/home/s4549287/db/rbs/rbs-catetory.tsv /srv/home/s4549287/db/group/RNA/model iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.bdy iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.ftr --fullseq-clf iter-0/all-fullseq-proba.tsv --group RNA --proba 0.5 --hallmark /srv/home/s4549287/db/group/RNA/hallmark-gene.list 2> $Log || { echo "See error details in $Log" | python /srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }
        else
            python /srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/prophage.py iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split iter-0/RNA/all.pdg.hmm.tax /srv/home/s4549287/db/rbs/rbs-catetory.tsv /srv/home/s4549287/db/group/RNA/model iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.bdy iter-0/RNA/all.pdg.gff.splitdir/all.pdg.gff.0.split.prv.ftr --fullseq-clf iter-0/all-fullseq-proba.tsv --group RNA --proba 0.5 2> $Log || { echo "See error details in $Log" | python /srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }
        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

Looking at the log file suggested:

Traceback (most recent call last): File "/srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/provirus.py", line 638, in main() File "/srv/home/s4549287/db/conda_envs/cadc5396/lib/python3.8/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/srv/home/s4549287/db/conda_envs/cadc5396/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/srv/home/s4549287/db/conda_envs/cadc5396/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/srv/home/s4549287/db/conda_envs/cadc5396/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/provirus.py", line 635, in main provirus_ins.find_boundary() File "/srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/provirus.py", line 572, in find_boundary self.process_one_contig(last_seqname, last_seqlen, mat) File "/srv/home/s4549287/.conda/envs/vs2/lib/python3.8/site-packages/virsorter/./scripts/provirus.py", line 312, in process_one_contig if pr_full < PROVIRUS_CHECK_MAX_FULLSEQ_PROBA and \ ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

The initial command was:

virsorter run -w /srv/projects/coral/Accelerate_project/analyses/20201002_viral_prep/20201218_VIRSorter2_RNA_viruses/ -i /srv/projects/coral/Accelerate_project/analyses/20201002_viral_prep/RNA_sequences/len1000contigs.fasta --include-groups "RNA" --min-length 1000 --prep-for-dramv

Do you have any pointers? Thanks, Megan

jiarong / VirSorter2

issue during virsorter2 run #29