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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Bug: Singularity image with get_seqs returning segfault #51

Closed j23414 closed 1 year ago

j23414 commented 1 year ago

Description

 .command.sh: line 28: 40309 Segmentation fault      (core dumped) get_seqs -e p_dups.bed p_Step_1_01_ArrowPolish_consensus.fasta -p pri
mary
...
  .command.sh: line 51: 40982 Segmentation fault      (core dumped) get_seqs -e h_dups.bed h_a_Step_1_01_ArrowPolish_consensus.fasta -p h
aps

Running the commands line by line in HPC worked using the Ceres modules purge_dups=1.2.5. The error only showed up when we used the singularity image. The singularity image also contained purge_dups=1.2.5.

j23414 commented 1 year ago

Looking at the end ofwork/long hash/.command.out log file, this was due to a slurm job timeout error:

Fixed by changing adding -t 48:00:00 to all [clusterOptions](https://github.com/isugifNF/polishCLR/blob/main/configs/slurm.config#L3) configs.