FileNotFoundError: [Errno 2] No such file or directory: 'test_metaG_ViWrap_out/00_VIBRANT_VirSorter_test_metaG/VirSorter_test_metaG/CheckV_result/quality_summary.tsv'

[Cczyf]

Hi,developer, thanks for your pipeline!

There is a issure about when I run the pipeline through the test file provided in Github, I am getting the following error messages showing checkv_quality_summary.txt is missing:

(/home/hongchang/db/ViWrap_conda_env/ViWrap) hongchang@node01:~/db/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 /home/hongchang/db/ViWrap_db --identify_method vb-vs --conda_env_dir /home/hongchang/db/ViWrap_conda_env --threads 40 --input_length_limit 5000

Welcome to ViWrap

The issued command is:
/home/hongchang/db/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 /home/hongchang/db/ViWrap_db --identify_method vb-vs --conda_env_dir /home/hongchang/db/ViWrap_conda_env --threads 40 --input_length_limit 5000

[2024-12-24 17:30:44] | Pre-check inputings. In processing...
[2024-12-24 17:30:46] | 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
[2024-12-24 17:30:46] | Run VIBRANT-VirSorter2 method. Run VIBRANT to identify and annotate viruses from input metagenome. In processing...
[2024-12-24 17:32:46] | Run VIBRANT-VirSorter2 method. Run VIBRANT to identify and annotate viruses from input metagenome. Finished
[2024-12-24 17:32:46] | 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...
[2024-12-24 18:35:06] | Run VIBRANT-VirSorter2 method. Run VirSorter2 to identify viruses from input metagenome. Finished
[2024-12-24 18:35:07] | Run VIBRANT-VirSorter2 method. Run CheckV to QC and trim viruses identified from VirSorter2. Finished
Traceback (most recent call last):
File "/home/hongchang/db/ViWrap/ViWrap", line 173, in
output = cli()
File "/home/hongchang/db/ViWrap/ViWrap", line 167, in cli
args"func"
File "/home/hongchang/db/ViWrap/scripts/master_run.py", line 346, in main
scripts.module.screen_virsorter2_result(inner_vs_outdir, keep1_list_file, keep2_list_file, discard_list_file, manual_check_list_file)
File "/home/hongchang/db/ViWrap/scripts/module.py", line 2114, in screen_virsorter2_result
with open(quality_summary, 'r') as lines:
FileNotFoundError: [Errno 2] No such file or directory: 'test_metaG_ViWrap_out/00_VIBRANT_VirSorter_test_metaG/VirSorter_test_metaG/CheckV_result/quality_summary.tsv'