Error with virsorter2

[senukobla]

I tried running virsorter2 but got the message below. Any ideas how I can resolve this

[2021-02-13 22:33 INFO] conig file written to /fs/ess/PES0842/Data/senu/config.yaml

[2021-02-13 22:33 INFO] Executing: snakemake --snakefile /users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/Snakefile --directory /fs/ess/PES0842/Data/senu --jobs 48 --configfile /fs/ess/PES0842/Data/senu/config.yaml --conda-prefix /fs/ess/PES0842/Applications/conda_envs --rerun-incomplete --use-conda --nolock --latency-wait 600 --quiet all
Job counts: count jobs 1 all 1 classify 5 classify_by_group 5 classify_full_and_part_by_group 1 extract_feature 1 extract_provirus_seqs 1 finalize 5 hmm_features_by_group 1 hmm_sort_to_best_hit_taxon 5 hmm_sort_to_best_hit_taxon_by_group 5 hmmsearch 5 hmmsearch_by_group 1 merge_classification 1 merge_full_and_part_classification 5 merge_hmm_gff_features_by_group 5 merge_provirus_call_by_group_by_split 1 merge_provirus_call_from_groups 3 merge_split_hmmtbl 20 merge_split_hmmtbl_by_group 3 merge_split_hmmtbl_by_group_tmp 1 pick_viral_fullseq 375 provirus_call_by_group_by_split 451 [2021-02-14 02:59 ERROR] See error details in log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log [Sun Feb 14 02:59:02 2021] Error in rule hmm_sort_to_best_hit_taxon: jobid: 26 output: iter-0/all.pdg.hmm.tax, iter-0/all.pdg.hmm.ftr log: log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log (check log file(s) for error message) conda-env: /fs/ess/PES0842/Applications/conda_envs/7a574821 shell:

    python /users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py 30 "iter-0/all.pdg.Archaea.hmmtbl,iter-0/all.pdg.Bacteria.hmmtbl,iter-0/all.pdg.Eukaryota.hmmtbl,iter-0/all.pdg.Mixed.hmmtbl,iter-0/all.pdg.Viruses.hmmtbl" "arc,bac,euk,mixed,vir" > iter-0/all.pdg.hmm.tax 2> log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log || { echo "See error details in log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log" | python /users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/echo.py --level error; exit 1; }
    python /users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/add-unaligned-to-hmm-featrues.py iter-0/all.pdg.faa iter-0/all.pdg.hmm.tax > iter-0/all.pdg.hmm.ftr
    
    (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

[jiarong]

Hi, thanks for the feedback. Can you paste the content of "log/iter-0/step2-extract-feature/extract-feature-from-hmmout-common.log" here?

[senukobla]

Traceback (most recent call last): File "/users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py", line 114, in main() File "/users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py", line 101, in main d_tblout = get_dict_whole_seq(tblout_lis, tag_lis)
File "/users/PES0842/senukobla1/anaconda3/lib/python3.7/site-packages/virsorter/./scripts/extract-feature-from-hmmout.py", line 45, in get_dict_whole_seq e_val = float(lis[4]) ValueError: could not convert string to float: '----'

[jiarong]

Looks like there is an issue with hmmer output formatting. I need to see the input files to find the problem. Could you upload the following files: iter-0/all.pdg.Archaea.hmmtbl iter-0/all.pdg.Bacteria.hmmtbl iter-0/all.pdg.Eukaryota.hmmtbl iter-0/all.pdg.Mixed.hmmtbl iter-0/all.pdg.Viruses.hmmtbl

[senukobla]

all.pdg.Archaea.txt all.pdg.Eukaryota.txt all.pdg.Bacteria.txt all.pdg.Mixed.txt all.pdg.Viruses.txt

[senukobla]

all.pdg.Archaea.txt all.pdg.Eukaryota.txt all.pdg.Bacteria.txt Uploading all.pdg.Mixed.txt…

[senukobla]

see files attached above . Sorry for the multiple posts. I think the first one has all the files

[senukobla]

Any updates on this problem . The files you requested are above

[jiarong]

Sorry for the delay. I found all.pdg.Bacteria.txt is corrupted, which might be caused by instability of hardware. Re-run the sample should resolve the problem.