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dib-lab / dammit

just annotate it, dammit!
http://dib-lab.github.io/dammit/
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Error when running dammit 0.0.8 #27

Closed ctb closed 8 years ago

ctb commented 8 years ago 
[ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

Error: Failed to open sequence file /nema/short.fa.transdecoder_dir/longest_orfs.pep for reading

Apparently it's under the dammit directory:

# find /nema -name longest_orfs.pep
/nema/short.fa.dammit/short.fa.transdecoder_dir/longest_orfs.pep
camillescott commented 8 years ago

Oh my, that's a problem. Will push a fix shortly. On Nov 20, 2015 8:42 AM, "C. Titus Brown" notifications@github.com wrote:

[ ] hmmscan:longest_orfs.pep.x.Pfam-A.hmm

Error: Failed to open sequence file /nema/short.fa.transdecoder_dir/longest_orfs.pep for reading

Apparently it's under the dammit directory:

find /nema -name longest_orfs.pep

/nema/short.fa.dammit/short.fa.transdecoder_dir/longest_orfs.pep

— Reply to this email directly or view it on GitHub https://github.com/camillescott/dammit/issues/27.

ctb commented 8 years ago

I can run tests fairly quickly at this point on master - let me know when.

camillescott commented 8 years ago

Hmm, I can't seem to reproduce this. Are you working from a polluted output dir?

On Fri, Nov 20, 2015 at 9:57 AM, C. Titus Brown notifications@github.com wrote:

I can run tests fairly quickly at this point on master - let me know when.

— Reply to this email directly or view it on GitHub https://github.com/camillescott/dammit/issues/27#issuecomment-158474522.

Camille Scott

Department of Computer Science Lab for Data Intensive Biology University of California, Davis

camille.scott.w@gmail.com

ctb commented 8 years ago

Seems to be because I'm running from another directory -- that is, if I do:

cd /nema
dammit annotate short.fa

things work fine; if, instead, I do:

cd /home
dammit annotate /nema/short.fa

I get the failure. This happens with both 0.0.8 and master.

camillescott commented 8 years ago

Ahh -- I can probably fix this with a call to os.path.abspath somewhere :)

ctb commented 8 years ago

On Sun, Nov 22, 2015 at 08:19:06PM -0800, Camille Scott wrote:

Ahh -- I can probably fix this with a call to os.path.abspath somewhere :)

I breathlessly await confirmation of such!

camillescott commented 8 years ago

Resolved in 0.0.10; closing.