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davidemms / OrthoFinder

Phylogenetic orthology inference for comparative genomics
https://davidemms.github.io/
GNU General Public License v3.0
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Error while executing MSA and gene trees #823

Open senramvx opened 1 year ago

senramvx commented 1 year ago

Hi, I`ve just got this error while running Orthofinder 2.5.4 (-M msa -t 64 -a 8) in a CentOS cluster. It seems the analysis is still going on, but should I be worried? Any idea about what may have caused this?

Thanks in advance.

Marcus

Inferring remaining multiple sequence alignments and gene trees

2023-05-21 15:09:33 : Done 0 of 53255 Traceback (most recent call last): File "scripts_of/parallel_task_manager.py", line 209, in Worker_RunCommands_And_Move File "scripts_of/trees_msa.py", line 262, in trim_fn File "scripts_of/trim.py", line 94, in main File "scripts_of/trim.py", line 35, in init IndexError: list index out of range 2023-05-22 07:57:20 : Done 1000 of 53255

davidemms commented 1 year ago

Hi Marcus

Are you able to share the full OrthoFinder output so I can see if there's any indication of the problem?

Best wishes David