ZongzhiWu
commented
2 years ago virsorter run --seqname-suffix-off --provirus-off --prep-for-dramv -w vs2 -i /lustre/home/wangjiawen/S18/virus/04checkv/virus.fasta --min-length 5000 -j 21 all [2022-08-24 10:58 INFO] VirSorter 2.2.3 [2022-08-24 10:58 INFO] /lustre/home/wangjiawen/.conda/envs/virsorter2/bin/virsorter run --seqname-suffix-off --provirus-off --prep-for-dramv -w vs2 -i /lustre/home/wangjiawen/S18/virus/04checkv/virus.fasta --min-length 5000 -j 21 all [2022-08-24 10:58 INFO] Using /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/site-packages/virsorter/template-config.yaml as config template [2022-08-24 10:58 INFO] conig file written to /lustre/home/wangjiawen/S18/virus/07AMGs/vs2/vs2/config.yaml
[2022-08-24 10:58 INFO] Executing: snakemake --snakefile /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/site-packages/virsorter/Snakefile --directory /lustre/home/wangjiawen/S18/virus/07AMGs/vs2/vs2 --jobs 21 --configfile /lustre/home/wangjiawen/S18/virus/07AMGs/vs2/vs2/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /lustre/home/wangjiawen/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 1 combine_linear_circular 2 combine_linear_circular_by_group 1 extract_feature 1 finalize 1 get_viral_combined 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 2 merge_annotation_table_by_group_from_split 1 merge_annotation_table_from_groups 1 merge_classification 2 merge_hmm_gff_features_by_group 6 merge_split_hmmtbl 12 merge_split_hmmtbl_by_group 12 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 63 [Wed Aug 24 10:58:44 2022] Error in rule circular_linear_split: jobid: 8 output: iter-0/pp-seqname-length.tsv conda-env: /lustre/home/wangjiawen/db/conda_envs/ba51c345 shell:
# prep_logdir
mkdir -p log/iter-0/step1-pp log/iter-0/step2-extract-feature log/iter-0/step3-classify
Cnt=$(grep -c '^>' /lustre/home/wangjiawen/S18/virus/04checkv/virus.fasta)
if [ ${Cnt} = 0 ]; then
echo "No sequnences found in contig file; exiting" | python /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/echo.py --level error
exit 1
fi
python /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/circular-linear-split.py /lustre/home/wangjiawen/S18/virus/04checkv/virus.fasta iter-0/pp-circular.fna.preext iter-0/pp-linear.fna iter-0/pp-seqname-length.tsv "||rbs:common" 5000
if [ ! -s iter-0/pp-circular.fna.preext ]; then
echo "No circular seqs found in contig file" | python /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/site-packages/virsorter/./scripts/echo.py
rm iter-0/pp-circular.fna.preext
else
python /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/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 /lustre/home/wangjiawen/.conda/envs/virsorter2/lib/python3.8/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
[2022-08-15 16:36 INFO] Executing: snakemake --snakefile /home1/jialh/tools/miniconda3/envs/vs2/lib/python3.6/site-packages/virsorter/Snakefile --directory /share/inspurStorage/home3/ZXMGroup/VIROME/G3compare/results/04UHGG/test.out --jobs 4 --configfile /share/inspurStorage/home3/ZXMGroup/VIROME/G3compare/results/04UHGG/test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /share/inspurStorage/home1/jialh/human_virome/tools/db/conda_envs --use-conda --quiet all
Job counts: count jobs 1 all 1 check_point_for_reclassify 1 circular_linear_split 1 classify 5 classify_by_group 5 classify_full_and_part_by_group 1 combine_linear_circular 5 combine_linear_circular_by_group 1 extract_feature 1 extract_provirus_seqs 1 finalize 1 gff_feature 5 gff_feature_by_group 5 hmm_features_by_group 1 hmm_sort_to_best_hit_taxon 5 hmm_sort_to_best_hit_taxon_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 5 merge_split_hmmtbl 25 merge_split_hmmtbl_by_group 25 merge_split_hmmtbl_by_group_tmp 1 pick_viral_fullseq 1 preprocess 1 split_faa 5 split_faa_by_group 5 split_gff_by_group 121 [Mon Aug 15 16:36:12 2022]
*** 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