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Update error codes for retrying SPAdes #355

Merged
merged 3 commits into from
Nov 25, 2022
Merged

Update error codes for retrying SPAdes #355

merged 3 commits into from
Nov 25, 2022

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mglubber
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@mglubber mglubber commented Nov 17, 2022 •
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Spades can also raise error 21 if it fails due to lack of memory. Currently, this is not caught in ErrorStrategy, so it won't automatically retry with more memory. I've added error 21 to the error code list so that it will be included

Relevant error code information:

Counting (kmer_data.cpp : 349) The reads contain too many k-mers to fit into available memory. You need approx. 68.1699GB of free RAM to assemble your dataset

  == Error ==  system call for: "['/usr/local/bin/spades-hammer', 'spades/corrected/configs/config.info']" finished abnormally, OS return value: 21

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/mag branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@mglubber
Add error code 21 to SPAdes retry list
eb5013d 
Spades can also raise error 21 if it fails due to lack of memory during spades-hammer. Currently, this is not caught in the ErrorStrategy, so it won't automatically retry with more memory.

Relevant error code:
Counting (kmer_data.cpp : 349) The reads contain too many k-mers to fit into available memory. You need approx. 68.1699GB of free RAM to assemble your dataset

  == Error ==  system call for: "['/usr/local/bin/spades-hammer', 'spades/corrected/configs/config.info']" finished abnormally, OS return value: 21
@mglubber
Update CHANGELOG.md
4d232d5
@mglubber mglubber changed the title Dev Update error codes for retrying SPAdes Nov 17, 2022
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github-actions bot commented Nov 18, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eff45ab

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.6
  • Run at 2022-11-18 08:04:23

d4straub
d4straub approved these changes Nov 18, 2022
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Hello there,
thanks for the fix, looks good to me!
You are welcome to merge the PR once the tests successfully finished.

@mglubber
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Hi - it looks like everything passed, but I don't think I have permissions to merge the PR

@jfy133 jfy133 merged commit 07b4985 into nf-core:dev Nov 25, 2022
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jfy133 commented Nov 25, 2022

As I have the power (boom, exploding fire hydrant)

@jfy133 jfy133 mentioned this pull request Feb 27, 2023
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