Error in rule classify_full_and_part_by_group:

[TiAmoTYX]

[2023-10-17 10:10 INFO] VirSorter 2.2.4
[2023-10-17 10:10 INFO] /usr/local/bin/virsorter run -w outputs -i ./data/ComND.Sep_final_Scaftigs.fasta --min-length 1500 -j 4 all
[2023-10-17 10:10 INFO] Using /content/VirSorter2/virsorter/template-config.yaml as config template
Traceback (most recent call last):
File "/usr/local/bin/virsorter", line 33, in
sys.exit(load_entry_point('virsorter', 'console_scripts', 'virsorter')())
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1659, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/usr/local/lib/python3.6/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/content/VirSorter2/virsorter/virsorter.py", line 369, in run_workflow
viral_gene_enrich_off=viral_gene_enrich_off,
File "/content/VirSorter2/virsorter/config.py", line 151, in make_config
groups_avail = os.listdir(f'{db_dir}/group')
FileNotFoundError: [Errno 2] No such file or directory: '/VirSorter2/db/group'
[55]

#增加hmmscan线程数提高运行速度
!virsorter config --set HMMSEARCH_THREADS=4
[86]
4 秒
!virsorter run -w outputs -i ./data/ComND.Sep_final_Scaftigs.fasta --min-length 1500 -j 4 all --db-dir /content/VirSorter2/db

output
[2023-10-17 10:38 INFO] VirSorter 2.2.4
[2023-10-17 10:38 INFO] /usr/local/bin/virsorter run -w outputs -i ./data/ComND.Sep_final_Scaftigs.fasta --min-length 1500 -j 4 all --db-dir /content/VirSorter2/db
[2023-10-17 10:38 INFO] Using /content/VirSorter2/virsorter/template-config.yaml as config template
[2023-10-17 10:38 INFO] conig file written to /content/VirSorter2/outputs/config.yaml

[2023-10-17 10:38 INFO] Executing: snakemake --snakefile /content/VirSorter2/virsorter/Snakefile --directory /content/VirSorter2/outputs --jobs 4 --configfile /content/VirSorter2/outputs/config.yaml --latency-wait 600 --rerun-incomplete --nolock --conda-frontend mamba --conda-prefix /content/VirSorter2/db/conda_envs --use-conda --quiet all
Job stats:
job count min threads max threads

---

all 1 1 1
classify 1 1 1
classify_full_and_part_by_group 2 1 1
finalize 1 1 1
merge_full_and_part_classification 1 1 1
total 6 1 1

[2023-10-17 10:38 ERROR] See error details in /content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-ssDNA.log
[Tue Oct 17 10:38:12 2023]
Error in rule classify_full_and_part_by_group:
jobid: 60
output: iter-0/ssDNA/viral.trim.clf
conda-env: /content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d
shell:

        Log=/content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-ssDNA.log
        Hallmark_list_f=/content/VirSorter2/db/group/ssDNA/hallmark-gene.list
        if [ -s $Hallmark_list_f ]; then
            python /content/VirSorter2/virsorter/./scripts/classify-trimed.py iter-0/ssDNA/all.pdg.gff iter-0/ssDNA/all.pdg.hmm.tax /content/VirSorter2/db/rbs/rbs-catetory.tsv /content/VirSorter2/db/group/ssDNA/model iter-0/viral-combined.fa iter-0/ssDNA/viral.trim.clf --group ssDNA --hallmark /content/VirSorter2/db/group/ssDNA/hallmark-gene.list 2> $Log || { echo "See error details in $Log" | python /content/VirSorter2/virsorter/./scripts/echo.py --level error; exit 1; }
        else
            python /content/VirSorter2/virsorter/./scripts/classify-trimed.py iter-0/ssDNA/all.pdg.gff iter-0/ssDNA/all.pdg.hmm.tax /content/VirSorter2/db/rbs/rbs-catetory.tsv /content/VirSorter2/db/group/ssDNA/model iter-0/viral-combined.fa iter-0/ssDNA/viral.trim.clf --group ssDNA 2> $Log || { echo "See error details in $Log" | python /content/VirSorter2/virsorter/./scripts/echo.py --level error; exit 1; }
        fi

        
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

[2023-10-17 10:38 ERROR] See error details in /content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-dsDNAphage.log
[Tue Oct 17 10:38:12 2023]
Error in rule classify_full_and_part_by_group:
jobid: 59
output: iter-0/dsDNAphage/viral.trim.clf
conda-env: /content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d
shell:

        Log=/content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-dsDNAphage.log
        Hallmark_list_f=/content/VirSorter2/db/group/dsDNAphage/hallmark-gene.list
        if [ -s $Hallmark_list_f ]; then
            python /content/VirSorter2/virsorter/./scripts/classify-trimed.py iter-0/dsDNAphage/all.pdg.gff iter-0/dsDNAphage/all.pdg.hmm.tax /content/VirSorter2/db/rbs/rbs-catetory.tsv /content/VirSorter2/db/group/dsDNAphage/model iter-0/viral-combined.fa iter-0/dsDNAphage/viral.trim.clf --group dsDNAphage --hallmark /content/VirSorter2/db/group/dsDNAphage/hallmark-gene.list 2> $Log || { echo "See error details in $Log" | python /content/VirSorter2/virsorter/./scripts/echo.py --level error; exit 1; }
        else
            python /content/VirSorter2/virsorter/./scripts/classify-trimed.py iter-0/dsDNAphage/all.pdg.gff iter-0/dsDNAphage/all.pdg.hmm.tax /content/VirSorter2/db/rbs/rbs-catetory.tsv /content/VirSorter2/db/group/dsDNAphage/model iter-0/viral-combined.fa iter-0/dsDNAphage/viral.trim.clf --group dsDNAphage 2> $Log || { echo "See error details in $Log" | python /content/VirSorter2/virsorter/./scripts/echo.py --level error; exit 1; }
        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

[TiAmoTYX]

Hi,how can i fix it?

[TiAmoTYX]

Log=/content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-ssDNA.log

Traceback (most recent call last):
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 275, in
main()
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 271, in main
clf_trim_ins.load_data()
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 82, in load_data
indice = [ int(i) for i in indice ]
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 82, in
indice = [ int(i) for i in indice ]
ValueError: invalid literal for int() with base 10: 'Scaffol'

[TiAmoTYX]

Log=/content/VirSorter2/outputs/log/iter-0/step3-classify/provirus-score-dsDNAphage.log

Traceback (most recent call last):
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 275, in
main()
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/content/VirSorter2/db/conda_envs/68f94c41bd29d12e5ee0ead52425fb8d/lib/python3.8/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 271, in main
clf_trim_ins.load_data()
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 82, in load_data
indice = [ int(i) for i in indice ]
File "/content/VirSorter2/virsorter/./scripts/classify-trimed.py", line 82, in
indice = [ int(i) for i in indice ]
ValueError: invalid literal for int() with base 10: 'Scaffol'

[TiAmoTYX]

My Fasta file data format is:

ComND.Nov_Scaffold1 flag=0 multi=153.0944 len=251320
CTGTGAGGAGCAGCGTAATCCCTGCGGCAATCATGGCTTGGCGGAAGATTATTCTCATGT

[jiarong]

Hi, you are pretty close to finding the issue. Fasta format require the header line to start with ">".

[TiAmoTYX]

Hi,
I have found the problem. The data format after my ">" has an item called 'Scaffold', and deleting this item will solve the problem. Thank you for your work.