No input files found all the time

[YoungerRen]

dears there are some issues about the enrichm. When I use enrichm to process my MAGs, it always reports the following error.

and i downloaded the enrichm v0.5.0,v0.6.3,v0.6.5,but all of them reported the error. and I have found some reported problems similar to this one, but my attempts to solve them have been unsuccessful, and no solution has been proposed for this type of problem. Can you tell me what to do? This problem has been bothering me for almost a week now . following code is my input code.

best Younger

[geronimp]

Hello Younger,

Would you be able to provide a view of what files are in the "bins" directory?

Kind regards, Joel

[YoungerRen]

ok, Joel!this is my bins directory: best Younger

[geronimp]

Thanks Younger, looks like everything is fine there,

My suspicion here is that the prodigal pipeline is failing silently, resulting in this misleading error. I'll need to fix this, but in the meantime would you also be able to check that prodigal is correctly installed on your server? If it is, let me know and I can dig a little further.

[YoungerRen]

Thanks, Joel. the prodigal is fine!i checked the prodigal version, and it showed it was fine! i do hope u can solve the issue, please let me know if u solve the issue! thanks.

best Younger

[geronimp]

Thanks Younger, just one last thing, would you be able to rerun adding --verbosity 5 in the command? this will help me narrow down exactly where the pipeline is failing.

[YoungerRen]

ok,Joel!
I tried again by adding --verbosity 5, the error was as following: [2024-09-20 16:08:39 PM] INFO: Command: /public/home/hcao/taolab/RenYong/miniconda3/envs/enrichm/bin/enrichm annotate --genome_directory /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/test --threads 96 --ko --pfam --cazy --orthologs --suffix .fna --output /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/bin_anno --verbosity 5 [2024-09-20 16:08:39 PM] INFO: Running the annotate pipeline [2024-09-20 16:08:39 PM] INFO: Running pipeline: annotate [2024-09-20 16:08:39 PM] INFO: Setting up for genome annotation [2024-09-20 16:08:39 PM] INFO: Calling proteins for annotation [2024-09-20 16:08:39 PM] INFO: - Calling proteins for 1 genomes [2024-09-20 16:08:39 PM] DEBUG: ls /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/test/.fna | sed 's/.fna//g' | grep -o '[^/]$' | parallel -j 5 prodigal -q -p meta -o /dev/null -d /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/bin_anno/genome_genes/{}.fna -a /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/bin_anno/genome_proteins/{}.faa -i /public/home/hcao/taolab/jiahui/2stalga-bac-beadEXP/neiwaiceng/Result/test/{}.fna > /dev/null 2>&1 [2024-09-20 16:08:40 PM] DEBUG: Finished [2024-09-20 16:08:40 PM] ERROR: No files found with .fna suffix in input directory Traceback (most recent call last): File "/public/home/hcao/taolab/RenYong/miniconda3/envs/enrichm/bin/enrichm", line 351, in run.run_enrichm(args, sys.argv) File "/public/home/hcao/taolab/RenYong/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/run.py", line 416, in run_enrichm pipeline(args) File "/public/home/hcao/taolab/RenYong/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/run.py", line 307, in run_annotate args.protein_files) File "/public/home/hcao/taolab/RenYong/miniconda3/envs/enrichm/lib/python3.7/site-packages/enrichm/annotate.py", line 875, in annotate_pipeline raise Exception("No input files found") Exception: No input files found

and the "test" directory was the new files i built to test the code, which include a fna file. best Younger