multiqc could not find my files

Question

[Aki]

Hi everyone, I was running MultiQC in my current directory where my fastp report files are located but could not get any result (No analysis results found. Cleaning up..). do you have any solutions?

[barslmn]

Multiqc looks for specific file names. Is fastp results there? Can you show a tree of your files or show the fastp files with find -type -f -name "*fastp.json"

[Aki]

Hi barslmn, there are only fastp report files.

tree
.
├── report_SRR*44.json
├── report_SRR*45.json
├── report_SRR*46.json
├── report_SRR*47.json
├── report_SRR*48.json
├── report_SRR*49.json
├── report_SRR*50.json

[barslmn]

These file names should end with "*fastp.json". Try renaming and running the multiqc again.

Answer 1

[Phil Ewels]

You can see the search patterns for every MultiQC module in the docs. The Fastp module searches for filenames ending in fastp.json (see docs)

Either rename your files, or create a config file for MultiQC where you overwrite this search pattern (see docs).

[Aki]

it work well. Thank you all.

[Phil Ewels]

Great! Please mark as the answer then (green tick).