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sagnikbanerjee15 / Finder

A fully automated gene annotator from RNA-Seq expression data
MIT License
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Finder Stops Running during psi class assembly #58

Open hopehealey opened 2 years ago

hopehealey commented 2 years ago

Hello,

I am trying to run Finder on a new genome. It is stalling out on the PSI class assembly (I think). The script stopped working in the middle of a 24 hour run and did not leave any hints for why it failed (running on 40 cpus). The combined.error file in the assemblies_psiclass_modified folder is empty. Have you encountered this issue before?

The end of the progress.log file:

2022-05-25 21:08:02,638 - finder -   INFO - Started processing data for Brain
2022-05-25 21:08:03,796 - finder -   INFO - Information collection about alignments completed

The end of the .err file created by SLURM

2022/05/25 18:06:08  info unpack layer: sha256:4653e19d0f327f247839d79f7b72e8b08765bd7f98aeb166ad548ec2092e8561
2022/05/25 18:06:13  info unpack layer: sha256:e42914e789575c71344172f78246dc0433a7ad67ec004b1073f31594b2355b1d
INFO:    Creating SIF file...
sagnikbanerjee15 commented 2 years ago

Hello @hopehealey,

Thank you so much for your interest in finder. I have encountered issues where finder did not finish but this is new to me. If psiclass was the issue then there should have been something in the assemblies_psiclass_modified folder. Could you please send me the final .error file? Also, it would be great if you could send me the output folder zipped at sagnikbanerjee15@gmail.com

Thank you.

hopehealey commented 2 years ago

Hi @sagnikbanerjee15, I just tried to send the error file and tar.gz via email. Hopefully, it'll work though the output folder is quite large. The error file in the assemblies_psiclass_modified is empty.