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chrisjackson-pellicle / hybpiper-nf

Nextflow and Singularity/Conda pipeline for running HybPiper (https://github.com/mossmatters/HybPiper)
GNU General Public License v3.0
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intronerate.py IndexError: list index out of range #9

Closed theo-allnutt-bioinformatics closed 1 year ago

theo-allnutt-bioinformatics commented 3 years ago

Hi,

this error caused the nextflow pipline to exit. The sample in question, 80069 has a genes_with_seqs.txt file with normal looking lines.

from intronerate task command.log:

Traceback (most recent call last): File "/HybPiper/intronerate.py", line 405, in main() File "/HybPiper/intronerate.py", line 349, in main genelist = [x.split()[0] for x in open('genes_with_seqs.txt').readlines()] File "/HybPiper/intronerate.py", line 349, in genelist = [x.split()[0] for x in open('genes_with_seqs.txt').readlines()] IndexError: list index out of range

I suspect that intronerate.py may have been opening the file while it was still being written by the previous nf task, due to slow I/O?

Thanks,

Theo

chrisjackson-pellicle commented 1 year ago

Hi Theo,

The hybpiper-nf pipeline has been updated to use HybPiper version 2. The intronerate.py script no longer exists in version 2, and your issue should no longer occur.

Cheers,

Chris