Error in MultiQC

i did multiqc on my data much times, but this time i got this erorr

[INFO   ]         multiqc : This is MultiQC v1.7
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching 'multiqc_WDir'
[ERROR  ]         multiqc : Oops! The 'fastqc' MultiQC module broke... 
  Please copy the following traceback and report it at 
  If possible, please include a log file that triggers the error - the last file found was:
Module fastqc raised an exception: Traceback (most recent call last):
  File "/usr/local/tools/_conda/envs/__multiqc@1.7/bin/multiqc", line 440, in multiqc
    output = mod()
  File "/usr/local/tools/_conda/envs/__multiqc@1.7/lib/python3.6/site-packages/multiqc/modules/fastqc/", line 44, in __init__
    self.parse_fastqc_report(f['f'], s_name, f)
  File "/usr/local/tools/_conda/envs/__multiqc@1.7/lib/python3.6/site-packages/multiqc/modules/fastqc/", line 179, in parse_fastqc_report
    self.fastqc_data[s_name]['basic_statistics'] = {d['measure']: d['value'] for d in self.fastqc_data[s_name]['basic_statistics']}
KeyError: 'basic_statistics'
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

whats the problem

1 Like

Hi @amir

Few items to check:

  1. Is the MultiQC report input type set to be the same as for your input data content? Meaning, if summarizing FastQC results, that needs to be specified on the MultiQC form. There are many options, and FastQC is not the default.

  2. Inputs need to be in text format. For FastQC these will be the “raw” result datasets, not the “html” datasets.

  3. This prior QA has more details that may help: How do you use MultiQC on FastQC files taken from SRA files?

Check those and if still having problems, post back a screenshot of the MultiQC tool form settings and a screenshot of one of the inputs you selected. We can dig deeper if needed after that.

I ran a few tests this morning at using the most current tool version:

  • Tool: MultiQC aggregate results from bioinformatics analyses into a single report (Galaxy Version 1.7))

and FastQC “raw data” inputs. Same tool form settings as yours. One test used non-hidden datasets, the other used hidden datasets. Both ran fine.

I would suggest trying these, in order:

  1. Review the job details page. Make sure all of your inputs are actually the raw data with no html results. I don’t think that is the problem, but is worth doing.

  2. Rerun. Maybe there was a transient cluster issue. I suspect this was the problem given your original error message posted. Output the log – it will contain more details if the job fails again.

  3. Submit the bug report at the server if the job fails again. You can add in a link to this post to help them with context. You’ll get a cc’d copy of the report. It might contain more information that can help you to troubleshoot.

I’m also pinging some of the admins at that server to see if they can help more from here: @hxr @bjoern.gruening


If i want to use MultiQC with Sailfish upload files what option should i choose in the field “Which tool was used generate logs” I do not see option for sailfish.

Thank you

Some tools does not have their own icon, Try Some other icons like RseqC, i really didn’t work with sailfish .Ask Director, he will tell you the right answer