FileNotFoundError: [Errno 2] No such file or directory: 'test_metaG_ViWrap_out/00_VIBRANT_VirSorter_test_metaG/VirSorter_test_metaG/pass/final-viral-score.tsv'

[LiZhihua1982]

(/mnt/FF/ViWrap_conda_environments/ViWrap2025) lizhihua@lizhihua-T640:/mnt/FF/ViWrap_conda_environments/ViWrap/example_data$ ViWrap run --input_metagenome test_metaG.fasta --input_reads reads_1.fastq.gz,reads_2.fastq.gz --out_dir test_metaG_ViWrap_out --db_dir /mnt/FF/ViWrap_db --identify_method vb-vs --conda_env_dir /mnt/FF/ViWrap_conda_environments --threads 20 --input_length_limit 5000 -t 20

Welcome to ViWrap

The issued command is:
/mnt/FF/ViWrap_conda_environments/ViWrap/ViWrap run --input_metagenome test_metaG.fasta --input_reads reads_1.fastq.gz,reads_2.fastq.gz --out_dir test_metaG_ViWrap_out --db_dir /mnt/FF/ViWrap_db --identify_method vb-vs --conda_env_dir /mnt/FF/ViWrap_conda_environments --threads 20 --input_length_limit 5000

[2025-01-11 18:38:56] | Pre-check inputings. In processing...
[2025-01-11 18:38:56] | Looks like the input metagenome and reads, database, and custom MAGs dir (if option used) are now set up well, start up to run ViWrap pipeline
[2025-01-11 18:38:56] | Run VIBRANT-VirSorter2 method. Run VIBRANT to identify and annotate viruses from input metagenome. In processing...
[2025-01-11 18:43:56] | Run VIBRANT-VirSorter2 method. Run VIBRANT to identify and annotate viruses from input metagenome. Finished
[2025-01-11 18:43:56] | Run VIBRANT-VirSorter2 method. Run VirSorter2 to identify viruses from input metagenome. Also plus CheckV to QC and trim, and KEGG, Pfam, and VOG HMMs to annotate viruses. In processing...
[2025-01-11 18:49:42] | Run VIBRANT-VirSorter2 method. Run VirSorter2 to identify viruses from input metagenome. Finished
[2025-01-11 18:49:43] | Run VIBRANT-VirSorter2 method. Run CheckV to QC and trim viruses identified from VirSorter2. Finished
Traceback (most recent call last):
File "/mnt/FF/ViWrap_conda_environments/ViWrap/ViWrap", line 173, in
output = cli()
File "/mnt/FF/ViWrap_conda_environments/ViWrap/ViWrap", line 167, in cli
args"func"
File "/mnt/FF/ViWrap_conda_environments/ViWrap/scripts/master_run.py", line 358, in main
scripts.module.screen_virsorter2_result(inner_vs_outdir, keep1_list_file, keep2_list_file, discard_list_file, manual_check_list_file)
File "/mnt/FF/ViWrap_conda_environments/ViWrap/scripts/module.py", line 2134, in screen_virsorter2_result
with open(final_viral_score, 'r') as lines:
FileNotFoundError: [Errno 2] No such file or directory: 'test_metaG_ViWrap_out/00_VIBRANT_VirSorter_test_metaG/VirSorter_test_metaG/pass/final-viral-score.tsv'

[brilliant2643]

Hi! I have encountered the same problem, did you solve it?

[yyyangzd]

Hi! I have encountered the same problem, did you solve it?

Hi, did you solve this?

[yyyangzd]

I think I have solved this problem. You need to revise the ViWrap-1.3.1/scripts/master_run.py script.

Search for all the key words "run_VirSorter2.py“ and then you will find the original code:
os.system(f"conda run -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python {os.path.join(args['root_dir'],'scripts/run_VirSorter2.py')} {header_replaced_input_metagenome} {args['virsorter_outdir']} {args['threads']} {args['input_length_limit']} >/dev/null 2>&1")

You have to change all the code involving "run_VirSorter2.py“ to:
os.system(f"conda run -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python {os.path.join(args['root_dir'],'scripts/run_VirSorter2.py')} {header_replaced_input_metagenome} {args['virsorter_outdir']} {args['threads']} {args['input_length_limit']}") (just remove the >/dev/null 2>&1)

After making this change, the issue has been resolved on my end.

[kangluyao]

I think I have solved this problem. You need to revise the ViWrap-1.3.1/scripts/master_run.py script.

Search for all the key words "run_VirSorter2.py“ and then you will find the original code: os.system(f"conda run -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python {os.path.join(args['root_dir'],'scripts/run_VirSorter2.py')} {header_replaced_input_metagenome} {args['virsorter_outdir']} {args['threads']} {args['input_length_limit']} >/dev/null 2>&1")

You have to change all the code involving "run_VirSorter2.py“ to: os.system(f"conda run -p {os.path.join(args['conda_env_dir'], 'ViWrap-vs2')} python {os.path.join(args['root_dir'],'scripts/run_VirSorter2.py')} {header_replaced_input_metagenome} {args['virsorter_outdir']} {args['threads']} {args['input_length_limit']}") (just remove the >/dev/null 2>&1)

After making this change, the issue has been resolved on my end.

Sadly, It does not work for me