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harmslab / topiary

Python framework for doing ancestral sequence reconstruction
MIT License
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No bootstrap MSA files written in "Alignment to Ancestors" step #43

Closed jmayoral1 closed 9 months ago

jmayoral1 commented 9 months ago

Greetings,

I've encountered an error that I can't quite figure out during the later bootstrapping portion of the "Alignment_to_Ancestors" phase of the pipeline. Per my error log, the bootstrap multiple sequence alignment files are not printed out in the "00_generate-replicates" working directory (or any directory for that matter). The bootstrap tree files are printed out just fine to the directory "00_generate-replicates", so seemingly the SLURM script can identify the appropriate directory. Perhaps it is an issue with the new version of raxml-ng? (I'm using v1.2, as opposed to v1.1).

Any assistance would be greatly appreciated! I've attached the errlog from SLURM. Happy to provide more information if needed.

Thank you for developing this neat tool.

Best, Josh

AlitoAnc_Script_errlog.txt

harmsm commented 9 months ago

Hi Josh,

Yes, this is an issue with the new raxml-ng. They changed the flags for bootstrap replicate and msa generation. For now, you could go back to raxml-ng 1.1 now (this requires manual installation rather than condo). I’m working on a patch, but we’re right at the end of our term, so I can’t finish until next week.

Best,

Mike

On Dec 1, 2023, at 09:12, jmayoral1 @.***> wrote:

Greetings,

I've encountered an error that I can't quite figure out during the later bootstrapping portion of the "Alignment_to_Ancestors" phase of the pipeline. Per my error log, the bootstrap multiple sequence alignment files are not printed out in the "00_generate-replicates" working directory (or any directory for that matter). The bootstrap tree files are printed out just fine to the directory "00_generate-replicates", so seemingly the SLURM script can identify the appropriate directory. Perhaps it is an issue with the new version of raxml-ng? (I'm using v1.2, as opposed to v1.1).

Any assistance would be greatly appreciated! I've attached the errlog from SLURM. Happy to provide more information if needed.

Thank you for developing this neat tool.

Best, Josh

AlitoAnc_Script_errlog.txt

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jmayoral1 commented 9 months ago

Hi Mike,

Thank you for the speedy reply! Downgrading to raxml-ng v1.1.0 indeed solved the problem. Closing this issue now.

Regards, Josh