Closed macmanes closed 8 years ago
Also, the longest_orfs.pep.pfam.tbl.out
file is similarly messed up. I'm also concerned that the large chunks of empty lines are spaces were real results should appear. Only about 10% of my proteins are in the output.. The 90% seems like they got lost someplace in the mix.
Yeah, I plan on pushing a new release today -- this error is fixed and tested in the current master branch. The fix is basically to write to /dev/stdout
instead of to a file.
This is now fixed in 0.3. A couple things to note though:
.tbl.out
file will still be messed up.
Easy to fix issue with the way you are handling the individual hmmscan jobs..
The command:
The error
The issue:
looking at
longest_orfs.pep.pfam.tbl
you get some hmmscan header info, many empty lines, the tabular output you actually want. This pattern over and over again.turns out, even with
--domtblout
you get some extra stuff in there that you probably don't want when merging multiple runs together.