I have minimised the threads but still cant run.

chmccarthy / Pangloss

Pangenome analysis of eukaryotes.

GNU General Public License v3.0

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I have minimised the threads but still cant run. #5

Open NeeluBegum opened 4 years ago

NeeluBegum commented 4 years ago

I keep getting this error when i run. It stops at INFO: PanGuess: Running Exonerate searches on 3 threads according to the log. I am just running the testconfig.ini

File "/anaconda2/envs/python2/lib/python2.7/multiprocessing/pool.py", line 572, in get raise self._value OSError: [Errno 13] Permission denied

chmccarthy commented 4 years ago

Hi Neelu,

I've responded to this elsewhere but just to repeat it here I think the issue is that Pangloss can't run Exonerate for some reason. Check that you can run Exonerate independently through the command line and that Exonerate has executable permissions.

qbdong commented 4 years ago

Hi, I have the same error with you. I can run Exonerate independently through the command line ,but I still got the error,like this File "/home/qbdong/miniconda3/envs/pangloss/lib/python2.7/multiprocessing/pool.py", line 567, in get raise self._value AssertionError How can I solve it? Thank you

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:

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

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:

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?

Sorry， I still don't solve my error, I'm sorry I can't help you