Hi, I'm having some problems using virsorter2. I don't know if it's done, because it isn't quit the program yet and looks like it's still running, this has been going on for a long time. Are there any other steps that need to be run?

[2021-10-20 22:09 INFO] /public/home/huqy/miniconda3/envs/viral-id-sop/bin/virsorter run --keep-original-seq -w A2_1.out -i A2_scaffolds.fasta --min-length 5000 --min-score 0.5 -j 6 all [2021-10-20 22:09 INFO] Using /public/home/huqy/miniconda3/envs/viral-id-sop/lib/python3.8/site-packages/virsorter/template-config.yaml as config template [2021-10-20 22:09 INFO] conig file written to /public/home/huqy/A2_1.out/config.yaml

[2021-10-20 22:09 INFO] Executing: snakemake --snakefile /public/home/huqy/miniconda3/envs/viral-id-sop/lib/python3.8/site-packages/virsorter/Snakefile --directory /public/home/huqy/A2_1.out --jobs 6 --configfile /public/home/huqy/A2_1.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /public/home/huqy/db-vs2/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 [2021-10-20 22:09 INFO] # of seqs < 5000 bp and removed: 311691 [2021-10-20 22:09 INFO] # of circular seqs: 68 [2021-10-20 22:09 INFO] # of linear seqs : 3731 [2021-10-20 22:09 INFO] Finish spliting circular contig file with common rbs [2021-10-20 22:09 INFO] Finish spliting linear contig file with common rbs [2021-10-20 22:17 INFO] Step 1 - preprocess finished. [2021-10-21 01:13 INFO] Step 2 - extract-feature finished. [2021-10-21 01:28 INFO] ====> VirSorter run (provirus mode) finished.

of full seqs (>=2 genes) as viral: 1146

        # of partial seqs (>=2 genes) as viral: 10
        # of short   seqs (< 2 genes) as viral: 3

        Useful output files:
            final-viral-score.tsv       ==> score table
            final-viral-combined.fa     ==> all viral seqs
            final-viral-boundary.tsv    ==> table with boundary info

            Suffix is added to seq names in final-viral-combined.fa:
            full    seqs (>=2 genes) as viral:  ||full
            partial seqs (>=2 genes) as viral:  ||partial
            short   seqs (< 2 genes) as viral:  ||lt2gene

        NOTES:
        Users can further screen the results based on the following 
            columns in final-viral-score.tsv:
            - contig length (length) 
            - hallmark gene count (hallmark)
            - viral gene % (viral) 
            - cellular gene % (cellular)
        The group field in final-viral-score.tsv should NOT be used
            as reliable taxonomy info

        <====

[2021-10-21 01:28 INFO] Step 3 - classify finished.

jiarong / VirSorter2

issues of run VirSorter2 #90

of full seqs (>=2 genes) as viral: 1146