Failed sanitize_fasta_header jobs with sqlite3.OperationalError: disk I/O error in Cactus Pangenome on WSL Ubuntu 20.04

[whelixw]

Failed sanitize_fasta_header jobs with sqlite3.OperationalError: disk I/O error in Cactus Pangenome on WSL Ubuntu 20.04

Issue Description

I'm encountering an issue with Cactus Pangenome where multiple sanitize_fasta_header jobs fail, leading to the entire workflow failing. This happens both with the precompiled binaries and with a version of Cactus I compiled myself. The error involves an sqlite3.OperationalError: disk I/O error, suggesting a problem with disk I/O operations within the SQLite database that Cactus uses. This issue occurs on Windows Subsystem for Linux (WSL) running Ubuntu 20.04.6 LTS.

Environment Details

• Cactus Version: Commit 000b287c651f32d7dea15be4937742d597ad57cf
• Toil Version: 6.0.0-0e2a07a20818e593bfdfde3cc51ca4ad809fde96
• Operating System: Ubuntu 20.04.6 LTS (Focal Fossa) under WSL
• Kernel Version: 4.4.0-22621-Microsoft #2506-Microsoft Fri Jan 01 08:00:00 PST 2016 x86_64 GNU/Linux
• Python Version: 3.8

Steps to Reproduce

The error occurs when running the following command as part of the Cactus Pangenome quickstart guide:

cactus-pangenome ./js ./examples/evolverPrimates.txt --outDir primates-pg --outName primates-pg --reference simChimp --vcf --giraffe --gfa --gbz --mapCores 1
[cactus_err_log.txt](https://github.com/ComparativeGenomicsToolkit/cactus/files/14374972/cactus_err_log.txt)

[glennhickey]

Looks like an issue with your filesystem. If you can move from a network to local drive that may help -- see this comment https://github.com/ComparativeGenomicsToolkit/cactus/issues/748#issuecomment-1315485579