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jasperlinthorst / reveal

Graph based multi genome aligner
MIT License
46 stars 3 forks source link

MULITMUMPICKER ERROR <type 'exceptions.UnboundLocalError'> #7

Closed fbemm closed 7 years ago

fbemm commented 7 years ago

I am trying to align a couple of finished genomes from the same species (<150Mb) and the the following error: MULITMUMPICKER ERROR <type 'exceptions.UnboundLocalError'>

Any ideas? Thanks F

jasperlinthorst commented 7 years ago

Hi, that's weird.. Are you using the latest commit? How do you invoke reveal? Does it also raise the exception when you run it on the small testcases that are in the test directory. E.g.

reveal align tests/1a.fa tests/1b.fa tests/1c.fa

Please let me know, so I can try to reproduce and fix this.

Cheers, Jasper

fbemm commented 7 years ago

My mistake. I invoked reveal with reveal $(ls *.fasta) ... Sorry!

fbemm commented 7 years ago

That was to fast. Two genomes are working, six don't if I invoke with reveal g1.fasta g2.fasta g3.fasta

jasperlinthorst commented 7 years ago

Indeed the way you invoke should be correct. Are you on the latest commit? Does the testcase with three genomes work or does that also give you problems?

fbemm commented 7 years ago

Test test set works fine. Just to be totally sure: g1, g2 and g3 can be multifasta files #3 ?

jasperlinthorst commented 7 years ago

That indeed should work, but that is what is causing the problem... :) I can reproduce it now, so I will fix it and let you know. Thanks!

jasperlinthorst commented 7 years ago

Ok, I fixed it and pushed it to github. Please let me know if its working for you..

jasperlinthorst commented 7 years ago

I spotted another problem with the same piece of code, which should now also be fixed. Can you let me know if it's working for you so I can close the issue? thanks.

fbemm commented 7 years ago

I think the error is fixed. I get a segfault now but that might be related to data amount / genome number. Thanks!