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bcftools module error with bcfstools stats output from version 1.3.1 #1832

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xiamaz opened this issue Dec 30, 2022 · 0 comments · Fixed by #1833
Closed

bcftools module error with bcfstools stats output from version 1.3.1 #1832

xiamaz opened this issue Dec 30, 2022 · 0 comments · Fixed by #1833

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@xiamaz
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xiamaz commented Dec 30, 2022

Description of bug

bcftools exits with an index-not found error when parsing bcftools output from version 1.3.1, this is caused by certain columns in the PSC output to be missing.

File that triggers the error

bcftools_stats_output.txt

MultiQC Error log

> multiqc testlogs/

  /// MultiQC 🔍 | v1.13

|           multiqc | Search path : /Users/max/testlogs
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 1/1
╭──────────────────────────────────── Oops! The 'bcftools' MultiQC module broke... ────────────────────────────────────╮
│ Please copy this log and report it at https://github.com/ewels/MultiQC/issues                                        │
│ Please attach a file that triggers the error. The last file found was: testlogs/bcftools_stats_output.txt            │
│                                                                                                                      │
│ Traceback (most recent call last):                                                                                   │
│   File "/usr/local/lib/python3.9/site-packages/multiqc/multiqc.py", line 654, in run                                 │
│     output = mod()                                                                                                   │
│   File "/usr/local/lib/python3.9/site-packages/multiqc/modules/bcftools/bcftools.py", line 40, in __init__           │
│     n["stats"] = self.parse_bcftools_stats()                                                                         │
│   File "/usr/local/lib/python3.9/site-packages/multiqc/modules/bcftools/stats.py", line 121, in parse_bcftools_stats │
│     nMissing = int(s[13].strip())                                                                                    │
│ IndexError: list index out of range                                                                                  │
│                                                                                                                      │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
|           multiqc | No analysis results found. Cleaning up..
|           multiqc | MultiQC complete
ewels added a commit to MultiQC/test-data that referenced this issue Dec 30, 2022
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