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FASTP misses paired end JSON files #2333

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adamrtalbot opened this issue Feb 15, 2024 · 0 comments · Fixed by #2334
Closed
4 tasks done

FASTP misses paired end JSON files #2333

adamrtalbot opened this issue Feb 15, 2024 · 0 comments · Fixed by #2334

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@adamrtalbot
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adamrtalbot commented Feb 15, 2024

Description of bug

When using MultiQC on a JSON file produced by fastp 0.23.4 on paired end reads, it misses the logs.

It's because it's looking for the string '"before_filtering": {' which occurs on line 5, but stops at line 3 (not sure about indexing here).

fastp:
fn: "*.json"
contents: '"before_filtering": {'
num_lines: 3

File that triggers the error

SRR6357070_10.fastp.json

MultiQC Error log

multiqc .

  /// MultiQC 🔍 | v1.20

|           multiqc | Search path : /Users/adam.talbot/multiqc_fastp_bug
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 6/6
|           multiqc | No analysis results found. Cleaning up..
|           multiqc | MultiQC complete

Before submitting

  • I have read the troubleshooting documentation.
  • I am using the latest release of MultiQC.
  • I have included a full MultiQC log, not truncated.
  • I have attached an input file (.zip if necessary) that triggers the error.
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