fastp KeyError with --template sections option

[hmkim]

Description of bug

multiqc_data.json.zip

File that triggers the error

No response

MultiQC Error log

a  /// MultiQC 🔍 | v1.11

|           multiqc | Using log filenames for sample names
|           multiqc | Report title: Analysis Report
|           multiqc | Only using modules: picard, samtools, cutadapt, snpeff, fastp
|           multiqc | Search path : /data04/project/brandon/TBD211331-13734-WES-Mouse-brandon-20211129
|         searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 1440/1440
|            snpeff | Found 13 reports
|            picard | Found 13 MarkDuplicates reports
|          samtools | Found 39 flagstat reports
|          cutadapt | Found 13 reports
╭────────────────────────────────────────── Oops! The 'fastp' 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: ./multiqc_data_2/multiqc_data.json                      │
│                                                                                                                                │
│ Traceback (most recent call last):                                                                                             │
│   File "/TBI/People/tbi/isaac/.local/lib/python3.6/site-packages/multiqc/multiqc.py", line 624, in run                         │
│     output = mod()                                                                                                             │
│   File "/TBI/People/tbi/isaac/.local/lib/python3.6/site-packages/multiqc/modules/fastp/fastp.py", line 47, in __init__         │
│     self.parse_fastp_log(f)                                                                                                    │
│   File "/TBI/People/tbi/isaac/.local/lib/python3.6/site-packages/multiqc/modules/fastp/fastp.py", line 161, in parse_fastp_log │
│     cmd = parsed_json["command"].split()                                                                                       │
│ KeyError: 'command'                                                                                                            │
│                                                                                                                                │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
|           multiqc | Compressing plot data
|           multiqc | Previous MultiQC output found! Adjusting filenames..
|           multiqc | Use -f or --force to overwrite existing reports instead
|           multiqc | Report      : multiqc_report_4.html
|           multiqc | Data        : multiqc_data_4
|           multiqc | MultiQC complete

[ewels]

Hi @hmkim,

I'm a bit puzzled by this: The last file found was: ./multiqc_data_2/multiqc_data.json

So it sounds like the file causing this error is multiqc_data.json, which looks like an output file from a previous MultiQC run.

The default fastp module search pattern is '*fastp.json', so this file shouldn't be picked up by MultiQC. Are you overwriting this search pattern?

My suspicion is that this isn't an error with MultiQC, but rather just that your config is causing it to pick up an unexpected file by accident. Fixing the config to avoid this file should fix the error if that's the case.

Phil

[ewels]

Ok, I've updated the default MultiQC config to ignore any files called multiqc_data.json - hopefully that will indirectly solve your problem.

Let me know if you hit this issue again with a different file.

Phil

[hmkim]

Thank you Phil!