FileNotFoundError: [Errno 2] No such file or directory: '/lustre/isaac/proj/UTK0002/PALAVAS/PALAVAS_ViWrap/00_VIBRANT_VirSorter_PHYCOVIR_MEGAVIROME.contigs/VirSorter_PHYCOVIR_MEGAVIROME.contigs/pass/final-viral-score.tsv'

[eechase]

Hello !

I am getting the following error when I run the pipeline.

Traceback (most recent call last):
File "./ViWrap", line 173, in
output = cli()
File "./ViWrap", line 167, in cli
args"func"
File "/lustre/isaac/proj/UTK0002/SOFTWARES/ViWrap/scripts/master_run.py", line 332, in main
scripts.module.screen_virsorter2_result(inner_vs_outdir, keep1_list_file, keep2_list_file, discard_list_file, manual_check_list_file)
File "/lustre/isaac/proj/UTK0002/SOFTWARES/ViWrap/scripts/module.py", line 2096, in screen_virsorter2_result
with open(final_viral_score, 'r') as lines:
FileNotFoundError: [Errno 2] No such file or directory: '/lustre/isaac/proj/UTK0002/PALAVAS/PALAVAS_ViWrap/00_VIBRANT_VirSorter_PHYCOVIR_MEGAVIROME.contigs/VirSorter_PHYCOVIR_MEGAVIROME.contigs/pass/final-viral-score.tsv'

My input was:

./ViWrap run --input_metagenome /lustre/isaac/proj/UTK0002/PALAVAS/PHYCOVIR_MEGAVIROME.contigs.fa --input_reads /lustre/isaac/proj/UTK0002/PALAVAS/DATA/MEGA_FOR_PALAVAS.fastq --out_dir /lustre/isaac/proj/UTK0002/PALAVAS/PALAVAS_ViWrap --db_dir /lustre/isaac/proj/UTK0002/DATABASE/ViWrap --identify_method vb-vs --conda_env_dir /lustre/isaac/proj/UTK0002/conda/envs/ViWrap --threads 20 --input_length_limit 5000

Thanks for any input you have, happy to trouble shoot however. I did not notice any specific problems with the installation etc, so not too sure....

Emily

[seanyao97]

Hello, I also encountered the same problem, may I ask you to solve it

[jonbakerlab]

Also having the same problem let me know if somebody figures this one out.

[seanyao97]

I have switched to using the geNomad method for predictions and have obtained satisfactory feedback on the data.

[Chuen-Lee]

I had the same issue. I solved it by installing pandas into the virsorter environment.

micromamba activate /path/to/conda-env/ViWrap/ViWrap-vs2
micromamba install -c anaconda pandas

micromamba and conda should work exactly the same for this purpose. Not sure if installing pandas into the ViWrap conda-env directory would work the same. Good luck!