align_DNA failing

[philliplab]

A galosh profile is built. Then when I try to align_DNA one of the element sequences used to build the galosh profile back to the profile, the program hangs (just runs at 100% cpu and produces no output).

The commands (2nd one hangs):

profuse/alignedFastaToProfile_DNA cap008_profile.fasta consensus.fasta profile.galosh

profuse/align_DNA profile.galosh profile_element.fasta

Will upload the files in comments to this issue

[philliplab]

cap008_profile.txt

[philliplab]

consensus.txt

[philliplab]

profile_element.txt

[philliplab]

these are fasta files, I just had to change the extension to .txt for github