e.g.
Command line argument error: Argument "query". File is not accessible: `../Reference_Genes/reference_genes_n47.faa'
Traceback (most recent call last):
File "/home/lee/miniconda3/envs/backblast/share/backblast/scripts/search.py", line 308, in <module>
main(cli_args)
File "/home/lee/miniconda3/envs/backblast/share/backblast/scripts/search.py", line 213, in main
forward_blast_high_scoring_pairs = get_blast_hight_scoring_pairs(query_gene_cluster_path=query_gene_cluster_path,
File "/home/lee/miniconda3/envs/backblast/share/backblast/scripts/search.py", line 45, in get_blast_hight_scoring_pairs
return filter_blast_csv(run_blastp(query_gene_cluster_path,
File "/home/lee/miniconda3/envs/backblast/share/backblast/scripts/search.py", line 62, in run_blastp
blast_out = subprocess.check_output(
File "/home/lee/miniconda3/envs/backblast/lib/python3.9/subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "/home/lee/miniconda3/envs/backblast/lib/python3.9/subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['blastp', '-query', '../Reference_Genes/reference_genes_n47.faa', '-subject', './deltaproteobacterium_NaphS2.faa', '-evalue', '1e-25', '-soft_masking', 'true', '-seg', 'yes', '-outfmt', '10 qseqid sseqid pident evalue qcovhsp bitscore']' returned non-zero exit status 1.
Check if the input files are there in Python and error out with a clear message before calling BLASTp.