MultiQC not generating ouput ?

Question

[sunnykevin97]

Hello, I installed MultiQC running with python2.7 env, it not generating output ? Suggestions!

multiqc --file-list /home/doc/fastqgz/file_list.txt -o /home/doc/fastqgz/

[INFO ] multiqc : This is MultiQC v1.8
[INFO ] multiqc : Template : default
[WARNING] multiqc : You are running MultiQC with Python 2.7.17
[WARNING] multiqc : Please upgrade! MultiQC will soon drop support for Python < 3.6
[INFO ] multiqc : Searching : /home/doc/fastqgz/10_S9_R1_001.fastq.gz
[INFO ] multiqc : Searching : /home/doc/fastqgz/11_S13_R1_001.fastq.gz
[INFO ] multiqc : Searching : /home/doc/fastqgz/12_S17_R1_001.fastq.gz
[INFO ] multiqc : Searching : /home/doc/fastqgz/13_S21_R1_001.fastq.gz
[WARNING] multiqc : No analysis results found. Cleaning up..
[INFO ] multiqc : MultiQC complete

[ATpoint]

Suggestions!

Maybe there are no analysis results, because...read the warning:

[WARNING] multiqc : No analysis results found. Cleaning up..

You seem to search fastq files for analysis results, this makes no sense. Which results are you even looking for? fastqc?

[sunnykevin97]

I'm looking for fastqc analysis.

[H.Hasani]

yes, but according to output you are not.

[INFO ] multiqc : Searching : /home/doc/fastqgz/10_S9_R1_001.fastq.gz

[sunnykevin97]

I give a list of fastq.gz files to scan them, provided output directory, what wrong with this Really , I didn't understand. Please elaborate.

Answer 1

[ATpoint]

multiqc collects summary statistics from existing summary files, it does not run any QC analysis itself. You still have to run other QC tools before. multiqc can then be used to collect their output statistics and put them into a handy and human-readable html file. Therefore again: What analysis do you want to do on these files? Is it fastqc? If so run fastqc on all the fastq files, then go into the folder where the output results are and type multiqc .. This will then collect the fastqc output and make a nice summary.

Answer 2

[Arup Ghosh]

Multiqc does not run FastQC first you have to run the tool to generate quality reports for all the fastq files. Then combine the reports using Multiqc.

[sunnykevin97]

I'm confused, thanks for good explanation.