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
# 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 [ ${Cnt} = 0 ]; then
echo "No sequnences found in contig file; exiting" | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py --level error
exit 1
fi
python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/circular-linear-split.py /home/tian/meta/seq/test.fa iter-0/pp-circular.fna.preext iter-0/pp-linear.fna iter-0/pp-seqname-length.tsv "||rbs:common" 1500
if [ ! -s iter-0/pp-circular.fna.preext ]; then
echo "No circular seqs found in contig file" | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py
rm iter-0/pp-circular.fna.preext
else
python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/circular-extend.py iter-0/pp-circular.fna.preext iter-0/pp-circular.fna
fi
if [ ! -s iter-0/pp-linear.fna ]; then
echo "No linear seqs found in contig file" | python /home/tian/mambaforge/envs/virsort/lib/python3.10/site-packages/virsorter/./scripts/echo.py
rm iter-0/pp-linear.fna
fi
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Exiting because a job execution failed. Look above for error message
*** An error occurred. Detailed errors may not be printed for certain rules. Refer to the log file of the failed command for troubleshooting
Issues can be raised at: https://github.com/jiarong/VirSorter2/issues
Or send an email to virsorter2 near gmail.com if you do not use GitHub
Hi, this is a common issue reported caused by some system setting outside VS2. You can try installation option 3. It should be able to solve this issue.
Hi,
I am using test data from https://raw.githubusercontent.com/jiarong/VirSorter2/master/test/8seq.fa to have a demo test. there is my issue during this process, could you please help me solve that. my commend (virsort) tian@shpc-49085-instance-9CGQWKG0:~/mambaforge/envs/virsort$ 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
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:
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
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