hmmsearch error: Failed to open sequence file

Question

[zoepklein]

Hi, I'm trying to run hmmsearch against the Pfam database.

hmmsearch Pfam-A.hmm isoform_AA_0.fa gives me an error "Error: Failed to open sequence file isoform_AA_0.fa for reading"

[Mensur Dlakic]

How do you know that there is nothing wrong with the file? An error that you showed clearly indicates that the file is not present in that directory, or is not available for reading. It may help if you show us the output of the following two commands:

ls -al Pfam-A.hmm isoform_AA_0.fa
head -n 2 Pfam-A.hmm isoform_AA_0.fa