Hello, I'm trying to convert a hmmsearch output to gff format. For this, I ran the following:
hmmsearch --domtblout dom_results.txt --cpu 10 hydrocarbon.hmm orfs_file.faai > demo.log
After getting the dom_Results.txt table, I ran the hmmer2gff program from the mgkit program:
hmmer2gff -d -o demo.gff orfs.faa dom_results.txt
But I'm getting the following error message:
INFO - mgkit.io.fasta: Reading fasta file orfs.faa INFO - mgkit.io.fasta: Read 6846732 fasta sequences INFO - mgkit.workflow.hmmer2gff: Parsing HMMER data from file dom_results.txt INFO - mgkit.workflow.hmmer2gff: Writing GFF data to file demo.gff Traceback (most recent call last): File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/bin/hmmer2gff", line 11, in <module> sys.exit(main()) File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python2.7/site-packages/mgkit/workflow/hmmer2gff.py", line 212, in main options File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python2.7/site-packages/mgkit/workflow/hmmer2gff.py", line 178, in parse_domain_table_contigs noframe=options.no_frame, File "/Users/valentin-ignacio/opt/miniconda3/envs/mgkit/lib/python2.7/site-packages/mgkit/io/gff.py", line 1439, in from_hmmer contig, frame = line[0].rsplit('-', 1) ValueError: need more than 1 value to unpack
what can be the error here ?
Thanks for your time :)
