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Okay, I now see that the output from MAG for the f...
# meta-omics
t
Okay, I now see that the output from MAG for the fastqc process is only html files, not the fastqc data, behind the html files. So I need to run fastqc on the cleaned data, and then run multiqc. That I might get the txt file I want
j
Ahh I'm following now!
Yes, exactly
Sorry for the confusion of the txt files, the 
yaml
file is now default
I ran an older verison of taxprofiler
n
If you still have the work directories you may be able to get the fastqc files from there
this 1
t
Okay good that we are on the same page now 🙂
j
And yes, mag only saves the HTML files, I assume based on the assumption that if something looks wrong you need to go do a manual deepdive anyway. We could modify this though
t
Well, how do I find the 100 directories with the fastqc in the work directory. @Niklas Schandry not sure if I know how
n
You can use the .nextflow.log file
j
And Niklas is right - if you don't have the console output of the run anymore, you can cehck the 
piupeline_info
folder
somewhere there is the 
execution_report
I think it's called (a HTML)
n
and kind of grep for process name to find all fastqc processes
j
That has a table of all the processes
(Niklas is also right, I'm giving the more user friendly route ; ) )
t
Okay, thanks, yes I have those. I will try pulling out the fastqc folders and do it like that.
j
You can get the 
hash
directory form there
image.png
n
if james has a friendlier way use that, the log is kind of annoying to work with in my experience
j
From 
pipeline_info/execution_report_2025-10-13_12-28-09.html
Change into that, and hopefully if you didn't have clean up yuou can access it 🙂
t
Excellent, thanks guys I think I get the how I can get those data now. let's try it 🙂
👍 1
Hey, this worked @James Fellows Yates I managed to get to the exact samples with too much overrepresented reads. Now I know where my issues is and which datasets were a problem for me. Thanks for the help again, and also to @Niklas Schandry
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