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nanostat: crash when quality scores are missing #1717

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phue opened this issue Jul 1, 2022 · 0 comments · Fixed by #1718
Closed

nanostat: crash when quality scores are missing #1717

phue opened this issue Jul 1, 2022 · 0 comments · Fixed by #1718

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@phue
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phue commented Jul 1, 2022

Description of bug

The nanostat module breaks when reports were obtained from bam/cram files that have no qscores (i.e when plain fasta reads were used for mapping).

Currently, the nanostat module checks if the stats were obtained from alignments and calls reads_by_quality_plot(), which then throws the error below.

File that triggers the error

foo.bam_NanoStats.txt

MultiQC Error log

╭──────────────── Oops! The 'nanostat' 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:       │
│ ./foo_bam_NanoStats.txt                                                  │
│                                                                              │
│ Traceback (most recent call last):                                           │
│   File "/opt/conda/lib/python3.10/site-packages/multiqc/multiqc.py", line 65 │
│     output = mod()                                                           │
│   File "/opt/conda/lib/python3.10/site-packages/multiqc/modules/nanostat/nan │
│     self.reads_by_quality_plot()                                             │
│   File "/opt/conda/lib/python3.10/site-packages/multiqc/modules/nanostat/nan │
│     reads_gt = data_dict[data_key]                                           │
│ KeyError: '>Q5_aligned'                                                   │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯
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