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chmccarthy / Pangloss

Pangenome analysis of eukaryotes.
GNU General Public License v3.0
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Issue Running exonerate on second fasta in genomes.txt #7

Open JamiePike opened 4 years ago

JamiePike commented 4 years ago

Hello,

I am also having an issue with exonerate. Although this may be a problem with my set up.

I have run Pangloss successfully on the test data. However, if I run it on my data I get an error message when performing gene prediction on the second fasta listed in genomes. txt.

With this error:

image

Pangloss successfully performs gene prediction for the first fasta in genome.txt, but stops at 'INFO:PanGuess: Running Exonerate searches on 9 threads' on the second fasta.

I have so far been unable to work out why it will not run on the second fasta. I have tried swapping the second fasta for others, but it still fails on the second. Are you able to help?

qbdong commented 4 years ago

Hey, have you ever had a problem like this:

Can't load '~/miniconda3/lib/site_perl/5.26.2/x86_64-linux-thread multi/auto/Cwd/Cwd.so' for module Cwd: Traceback (most recent call last): IOError: [Errno 2] No such file or directory: 'genemark.gtf'

I just struggle for this error for a long time but still don't know how to solve it . Do you have any ideas?