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SPADES with exit code 12 when running out of memory #675

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bawee opened this issue Sep 23, 2024 · 3 comments · Fixed by #676
Closed

SPADES with exit code 12 when running out of memory #675

bawee opened this issue Sep 23, 2024 · 3 comments · Fixed by #676
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@bawee
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bawee commented Sep 23, 2024

Description of the bug

Hello,

SPADES seems to be exiting with exit code 12 when it runs out of memory. I wonder if this should be added to the exit codes that the pipeline recognises to retry SPADES with more RAM? Please see attached report.txt.

Thanks!

Command used and terminal output

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Relevant files

pipeline_report.txt

System information

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@bawee bawee added the bug Something isn't working label Sep 23, 2024
@jfy133
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jfy133 commented Sep 23, 2024 •
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Hi @bawee ! Yup good idea!

@jfy133 jfy133 linked a pull request Sep 23, 2024 that will close this issue
Add exit code 12 to SPAdes and standardise custom errorStragety formats #676
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@jfy133
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jfy133 commented Sep 23, 2024

PR here: #676

@jfy133
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jfy133 commented Sep 24, 2024

Done! Will be in next release

@jfy133 jfy133 closed this as completed Sep 24, 2024
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Add exit code 12 to SPAdes and standardise custom errorStragety formats nf-core/mag
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@bawee @jfy133