Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

VirSorter2 is a DNA and RNA virus identification tool. It leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection.

• VirSorter2 Github / tutorial page

• Module Name: VirSorter2 (see the modules page for more information)
• Unusual environment variables set
  • VS2_HOME  installation directory
  • VS2_BIN       executable directory
  • VS2_DATA    sample data folder

Allocate an interactive session and run the program.
Sample session on a GPU node:

[user@biowulf ~]$ sinteractive --mem=100g --cpus-per-task=4 --gres=lscratch:50
[user@cn2379 ~]$ module load virsorter2
[+] Loading singularity  3.8.2  on cn0853
[+] Loading virsorter2  2.2.3
[user@cn2379 ~]$ mkdir -p /data/$USER/VirSorter2 && cd /data/$USER/VirSorter2

Configuring VirSorter2 (need to be done only once):

 
[user@cn2379 ~]$ wget https://osf.io/v46sc/download -O db.tgz 
[user@cn2379 ~]$ gunzip -c db.tgz | tar -xvf -
[user@cn2379 ~]$ vs2 config --init-source --db-dir=$PWD/db
[2021-09-30 06:23 INFO] VirSorter 2.2.3
[2021-09-30 06:23 INFO] /VirSorter/bin/virsorter config --init-source --db-dir=/data/user/db
[2021-09-30 06:23 INFO] Attention: can not write template-config.yaml in source directory:
/VirSorter/lib/python3.7/site-packages/virsorter
makeing a copy to user home direcotry:
/home/user/.virsorter/template-config.yaml

[2021-09-30 06:23 INFO] Using {template} as config template
[2021-09-30 06:23 INFO] saving /data/user/VirSorter2/db as DBDIR to config file /home/user/.virsorter/template-config.yaml

Running VirSorter2 on sample data:

[user@cn2379 ~]$ cp $VS2_DATA/* .
[user@cn2379 ~]$ vs2 run -w test.out -i test-for-sop.fa --min-length 1500 -j 4 all 
[2021-09-30 17:03 INFO] VirSorter 2.1
[2021-09-30 17:03 INFO] /miniconda/bin/virsorter run -w test.out -i test-for-sop.fa --min-length 1500 -j 4 all
[2021-10-04 06:24 INFO] VirSorter 2.2.3
[2021-10-04 06:24 INFO] /opt/conda/envs/vs2/bin/virsorter config --init-source --db-dir=./db
[2021-10-04 06:24 INFO] Attention: can not write template-config.yaml in source directory:
/opt/conda/envs/vs2/lib/python3.8/site-packages/virsorter
makeing a copy to user home direcotry:
/home/user/.virsorter/template-config.yaml

[2021-10-04 06:24 INFO] Using {template} as config template
[2021-10-04 06:24 INFO] saving /gs7/users/user/VirSorter2/db as DBDIR to config file /home/user/.virsorter/template-config.yaml
[user@cn0864 VirSorter2]$ ls db/conda_envs
[userga@cn0864 VirSorter2]$  vs2 run -w test.out -i test-for-sop.fa --min-length 1500 -j 4 all
[2021-10-04 06:24 INFO] VirSorter 2.2.3
[2021-10-04 06:24 INFO] /opt/conda/envs/vs2/bin/virsorter run -w test.out -i test-for-sop.fa --min-length 1500 -j 4 all
[2021-10-04 06:24 INFO] Using /home/user/.virsorter/template-config.yaml as config template
[2021-10-04 06:24 INFO] conig file written to /gs7/users/user/VirSorter2/test.out/config.yaml

[2021-10-04 06:24 INFO] Executing: snakemake --snakefile /opt/conda/envs/vs2/lib/python3.8/site-packages/virsorter/Snakefile --directory /gs7/users/user/VirSorter2/test.out --jobs 4 --configfile /gs7/users/user/VirSorter2/test.out/config.yaml --latency-wait 600 --rerun-incomplete --nolock  --conda-frontend mamba --conda-prefix /gs7/users/user/VirSorter2/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
[2021-10-04 06:26 INFO] # of seqs < 1500 bp and removed: 0
[2021-10-04 06:26 INFO] # of circular seqs: 0
[2021-10-04 06:26 INFO] # of linear seqs  : 7
[2021-10-04 06:26 INFO] No circular seqs found in contig file
[2021-10-04 06:26 INFO] Finish spliting linear contig file with common rbs
[2021-10-04 06:26 INFO] Step 1 - preprocess finished.
[2021-10-04 06:32 INFO] Step 2 - extract-feature finished.
[2021-10-04 06:33 INFO]
            ====> VirSorter run (provirus mode) finished.
            # of full    seqs (>=2 genes) as viral:     6
            # of partial seqs (>=2 genes) as viral:     1
            # of short   seqs (< 2 genes) as viral:     0

            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

            <====

[2021-10-04 06:33 INFO] Step 3 - classify finished.

Create a batch input file (e.g. virsorter2.sh). For example:

#!/bin/bash
set -e
module load virsorter2
cp $VS2_DATA/* .  
vs2 run -w test.out -i test-for-sop.fa --min-length 1500 -j 4 all

Submit this job using the Slurm sbatch command.

sbatch virsorter2.sh