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Modules ccs: IndexError: list index out of range #1583

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sguizard opened this issue Nov 11, 2021 · 0 comments
Closed

Modules ccs: IndexError: list index out of range #1583

sguizard opened this issue Nov 11, 2021 · 0 comments
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bug: module Bug in a MultiQC module

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@sguizard
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sguizard commented Nov 11, 2021

Description of bug

The modules ccs reports the following error:
IndexError: list index out of range

This is caused by a dictionary that remains empty:
https://github.com/ewels/MultiQC/blob/0cf235dff69a272e31f60af5a58ef5125914f282/multiqc/modules/ccs/ccs.py#L124-L126

File that triggers the error

alz.1perc.subreads.10000.chunk3.report.zip

MultiQC Error log

$ multiqc -f  .

  /// MultiQC 🔍 | v1.11

|           multiqc | Search path : /home/sguizard/Work/Dev/github/nf-core/isoseq/work/34/44d269a98f606c853fc2cf63890151
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 17/17  
|    custom_content | nf-core-isoseq-summary: Found 1 sample (html)
|               ccs | Found 3 reports
[]
╭──────────────────────────────────────────────────── Oops! The 'ccs' 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: ./alz.1perc.subreads.10000.chunk3.report.json                            │
│                                                                                                                                                 │
│ Traceback (most recent call last):                                                                                                              │
│   File "/home/sguizard/Work/Softwares/anaconda3/envs/bioinfo/lib/python3.9/site-packages/multiqc/multiqc.py", line 624, in run                  │
│     output = mod()                                                                                                                              │
│   File "/home/sguizard/Work/Softwares/anaconda3/envs/bioinfo/lib/python3.9/site-packages/multiqc/modules/ccs/ccs.py", line 40, in __init__      │
│     self.add_sections()                                                                                                                         │
│   File "/home/sguizard/Work/Softwares/anaconda3/envs/bioinfo/lib/python3.9/site-packages/multiqc/modules/ccs/ccs.py", line 145, in add_sections │
│     plot=bargraph.plot(plot_data, plot_cats, config),                                                                                           │
│   File "/home/sguizard/Work/Softwares/anaconda3/envs/bioinfo/lib/python3.9/site-packages/multiqc/plots/bargraph.py", line 104, in plot          │
│     if type(cats[0]) is str or type(cats[0]) is unicode:                                                                                        │
│ IndexError: list index out of range                                                                                                             │
│                                                                                                                                                 │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
|           multiqc | Compressing plot data
|           multiqc | Deleting    : multiqc_report.html   (-f was specified)
|           multiqc | Deleting    : multiqc_data   (-f was specified)
|           multiqc | Deleting    : multiqc_plots   (-f was specified)
|           multiqc | Report      : multiqc_report.html
|           multiqc | Data        : multiqc_data
|           multiqc | Plots       : multiqc_plots
|           multiqc | MultiQC complete
@MatthiasZepper MatthiasZepper self-assigned this Nov 12, 2021
@MatthiasZepper MatthiasZepper added the bug: module Bug in a MultiQC module label Nov 12, 2021
sguizard added a commit to sguizard/MultiQC that referenced this issue Nov 22, 2021
- attributes have been modified (+ "ccs_processing" at the beginning). The failing test has been fixed.
@sguizard sguizard mentioned this issue Nov 22, 2021
2 tasks
@ewels ewels closed this as completed Jan 27, 2022
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