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and use tmpdir consistently for me most important to get https://github.com/samtools/samtools/releases/tag/1.14 because of > Improved samtools sort use of temporary files, both tidying up if it fails and recovery when facing pre-existing temporary files. The old versions apparently do not delete files in /tmp for failed jobs which causes problems on my site (due to my resubmission strategy I have more failing jobs than other sites I guess).