FastQC KeyError for reports with zero reads

[ec-ho-ra-mos]

Description of bug

I am running MultiQC (from DockerHub) version 1.11. For some reason, I am getting the error "Sample had zero reads". Am I doing something wrong? My input files are 2 FastQC output folders (test run). Each output folder contains the following: icons and images for the 2 folders, and fastqc.fo, fastqc_data.txt, fastqc_report.html, and summary.txt for the files.

File that triggers the error

fastqc_data.txt

MultiQC Error log

My run commands are just:

multiqc <directory>

This is the error message:

/// MultiQC � | v1.11

| multiqc | Search path : 15_fastqc

| fastqc | Found 2 reports

| fastqc | Sample had zero reads: 'F1-1A_S1_R1_001'

| fastqc | Sample had zero reads: 'F1-1A_S1_R2_001'

╭───────────────── Oops! The 'fastqc' 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: 15_f │

│ astqc/F1-1A_S1_R2_001_fastqc/fastqc_data.txt │

│ │

│ Traceback (most recent call last): │

│ File "/usr/lib/python3.8/site-packages/multiqc/multiqc.py", line 624, in r │

│ output = mod() │

│ File "/usr/lib/python3.8/site-packages/multiqc/modules/fastqc/fastqc.py", │

│ self.sequence_content_plot() │

│ File "/usr/lib/python3.8/site-packages/multiqc/modules/fastqc/fastqc.py", │

│ for b in data[s_name]: │

│ KeyError: 'F1-1A_S1_R1_001' │

│ │

╰──────────────────────────────────────────────────────────────────────────────╯

| multiqc | No analysis results found. Cleaning up..

| multiqc | MultiQC complete

[ewels]

Hi @ec-ho-ra-mos,

Thanks for opening this issue. The "Sample has no reads" error is what it sounds like - your FastQC report was generated for an empty FastQ file that has no reads. So there is nothing to generate QC for.

However, MultiQC should handle this gracefully without the python error traceback that you saw. @ErikDanielsson has spotted this error and opened #1535 to fix it, which I will review soon.

Thanks for reporting!

Phil

[ewels]

Hi @ec-ho-ra-mos,

Finally got to this PR to take a look. I owe you an apology - when I ran your supplied report it's clear that your sample did have reads. This was a nasty subtle bug where the read counts were being overwritten because MultiQC assumed some values would be there. I guess you ran FastQC with several sections skipped: those missing values were incorrectly interpreted as zero reads and a bunch of values overwritten with zeros.

Anyway, long story short - should now be fixed in #1535. Let me know how you get on with it.

Thanks for reporting!

Phil

[ec-ho-ra-mos]

Dear Dr. Ewels, Thank you very much for your update regarding this issue. I forgot to send an update on my question but I have managed to solve my issue already. It turned out the HPC that I was using was an older version of FastQC. What I did was I installed the newest version of FastQC and the outputs were all compatible with the then-newest version of MultiQC. Thank you very much for your attention to this matter. Sincerely, Jherico GERONCA

…

------------------------------------------------ *Jherico GERONCA (Mr.)* Research Student Department of Molecular and Cellular Analysis Graduate School of Pharmaceutical Sciences Kyoto University ------------------------------------------------ [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> 10/11/21, 07:45:30 am

On Wed, Nov 10, 2021 at 7:17 AM Phil Ewels ***@***.***> wrote: Hi @ec-ho-ra-mos <https://github.com/ec-ho-ra-mos>, Finally got to this PR to take a look. I owe you an apology - when I ran your supplied report it's clear that your sample *did* have reads. This was a nasty subtle bug where the read counts were being overwritten because MultiQC assumed some values would be there. I guess you ran FastQC with several sections skipped: those missing values were incorrectly interpreted as zero reads and a bunch of values overwritten with zeros. Anyway, long story short - should now be fixed in #1535 <#1535>. Let me know how you get on with it. Thanks for reporting! Phil — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#1533 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOWFC6BWQJJPXKHHIGJQFPLULGMZJANCNFSM5CMDPWEQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[ewels]

Ok great - well either way, you discovered a genuine bug even if it was an edge case :) MultiQC should now work properly with the old version of FastQC as well as the newer version.