error in running test

[tianyi1616]

Hi,

I am using test data from https://raw.githubusercontent.com/jiarong/VirSorter2/master/test/8seq.fa to have a demo test. there is my issue during this process, could you please help me solve that.
my commend
(virsort) tian@shpc-49085-instance-9CGQWKG0:~/mambaforge/envs/virsort$ virsorter run -w test.out -i /home/tian/meta/seq/test.fa --min-length 1500 -j 4 all
issue:
[2024-04-30 16:39 INFO] VirSorter 2.2.4
[2024-04-30 16:39 INFO] /home/tian/mambaforge/envs/virsort/bin/virsorter run -w test.out -i /home/tian/meta/seq/test.fa --min-length 1500 -j 4 all
[2024-04-30 16:39 INFO] Using /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/template-config.yaml as config template
[2024-04-30 16:39 INFO] conig file written to /home/tian/mambaforge/envs/virsort/test.out/config.yaml

[2024-04-30 16:39 INFO] Executing: snakemake --snakefile /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/Snakefile --directory /home/tian/mambaforge/envs/virsort/test.out --jobs 4 --configfile /home/tian/mambaforge/envs/virsort/test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /home/tian/mambaforge/envs/virsort/db/conda_envs --use-conda --quiet all
Job counts:
count jobs
1 all
1 check_point_for_reclassify
1 circular_linear_split
1 classify
2 classify_by_group
2 classify_full_and_part_by_group
1 combine_linear_circular
2 combine_linear_circular_by_group
1 extract_feature
1 extract_provirus_seqs
1 finalize
1 gff_feature
2 gff_feature_by_group
2 hmm_features_by_group
1 hmm_sort_to_best_hit_taxon
2 hmm_sort_to_best_hit_taxon_by_group
1 merge_classification
1 merge_full_and_part_classification
2 merge_hmm_gff_features_by_group
2 merge_provirus_call_by_group_by_split
1 merge_provirus_call_from_groups
5 merge_split_hmmtbl
10 merge_split_hmmtbl_by_group
10 merge_split_hmmtbl_by_group_tmp
1 pick_viral_fullseq
1 preprocess
1 split_faa
2 split_faa_by_group
2 split_gff_by_group
61
Traceback (most recent call last):
File "/home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/circular-linear-split.py", line 6, in
import screed
ModuleNotFoundError: No module named 'screed'
[Tue Apr 30 16:40:01 2024]
Error in rule circular_linear_split:
jobid: 8
output: iter-0/pp-seqname-length.tsv
conda-env: /home/tian/mambaforge/envs/virsort/db/conda_envs/d8ac0b5b
shell:

    # prep_logdir
    mkdir -p log/iter-0/step1-pp log/iter-0/step2-extract-feature log/iter-0/step3-classify

    Cnt=$(grep -c '^>' /home/tian/meta/seq/test.fa)
    if [ ${Cnt} = 0 ]; then
        echo "No sequnences found in contig file; exiting"               | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py --level error
        exit 1
    fi 

    python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/circular-linear-split.py           /home/tian/meta/seq/test.fa           iter-0/pp-circular.fna.preext          iter-0/pp-linear.fna           iter-0/pp-seqname-length.tsv           "||rbs:common"           1500

    if [ ! -s iter-0/pp-circular.fna.preext ]; then
        echo "No circular seqs found in contig file"               | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py
        rm iter-0/pp-circular.fna.preext
    else
        python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/circular-extend.py               iter-0/pp-circular.fna.preext iter-0/pp-circular.fna
    fi

    if [ ! -s iter-0/pp-linear.fna ]; then
        echo "No linear seqs found in contig file"               | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py
        rm iter-0/pp-linear.fna
    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
Or send an email to virsorter2 near gmail.com if you do not use GitHub

thanks very much!
Tian

[jiarong]

Hi, this is a common issue reported caused by some system setting outside VS2. You can try installation option 3. It should be able to solve this issue.