Question: MultiQC not generating ouput ?
0
gravatar for sunnykevin97
12 months ago by
sunnykevin97140
sunnykevin97140 wrote:

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
rna-seq next-gen • 1.0k views
ADD COMMENTlink modified 12 months ago by ATpoint46k • written 12 months ago by sunnykevin97140

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?

ADD REPLYlink modified 12 months ago • written 12 months ago by ATpoint46k

I'm looking for fastqc analysis.

ADD REPLYlink written 12 months ago by sunnykevin97140

yes, but according to output you are not.

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

ADD REPLYlink modified 12 months ago • written 12 months ago by H.Hasani980

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.

ADD REPLYlink written 12 months ago by sunnykevin97140
3
gravatar for ATpoint
12 months ago by
ATpoint46k
ATpoint46k wrote:

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.

ADD COMMENTlink written 12 months ago by ATpoint46k
1
gravatar for Arup Ghosh
12 months ago by
Arup Ghosh2.8k
India
Arup Ghosh2.8k wrote:

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.

ADD COMMENTlink written 12 months ago by Arup Ghosh2.8k

I'm confused, thanks for good explanation.

ADD REPLYlink written 12 months ago by sunnykevin97140
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