Trimgalore/cutadapt not creating FastQC html reports

[yaaminiv]

I am running this mox script on Manchester C. gigas gonad WGBS data. The files trimmed, but none of the fastqc HTML reports were generated! I ran a similar script on the Hawaii data and got HMTL reports, so I'm not sure why that's not happening this time. How can I get these reports from my TrimGalore/cutadapt code (besides running FastQC separately)?

Hawaii run slurm
Manchester run slurm

edit: added correct slurm links

[kubu4]

This error message is in your Hawaii slurm:

  >>> Now running FastQC on the validated data zr3616_8_R1_val_1.fq.gz<<<

Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, <IN2> line 5536487816.

  >>> Now running FastQC on the validated data zr3616_8_R2_val_2.fq.gz<<<

Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, <IN2> line 5536487816.
Deleting both intermediate output files zr3616_8_R1_trimmed.fq.gz and zr3616_8_R2_trimmed.fq.gz

I don't have time ATM to investigate the error, but the other option is to run FastQC independently, like so. It will run on all files matching this pattern (*.fq.gz), so you don't need to run FastQC one-by-one on each file:

# Set CPU threads to use
threads=28

# Populate array with FastQ files
fastq_array=(*.fq.gz)

# Pass array contents to new variable
fastqc_list=$(echo "${fastq_array[*]}")

# Run FastQC
# NOTE: Do NOT quote ${fastqc_list}
fastqc \
--threads ${threads} \
--outdir ${output_dir} \
${fastqc_list}

[kubu4]

Per this TrimGalore Issue, they say the error message indicates that the command couldn't find FastQC.

Is there some possibility that FastQC isn't in your system $PATH any more?

[yaaminiv]

Yup, I don't think it's in my path anymore. I tried running the code you posted above without specifying the fastqc directory and my script failed. I'll add it back to my path!

[sr320]

Or..... always use the full path :)

On Sun, Feb 7, 2021 at 4:51 PM Yaamini Venkataraman < ***@***.***> wrote: Yup, I don't think it's in my path anymore. I tried running the code you posted above without specifying the fastqc directory and my script failed. I'll add it back to my path! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#1104 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABB4PN5AFXDTCJWVL23O3VTS54YOXANCNFSM4XDSX5OQ> .

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[kubu4]

Here's a "pro" tip when running SLURM scripts on Mox (or, any computer, really). Add this to the bottom of your SLURM script:

# Document programs in PATH
{
date
echo ""
echo "System PATH for $SLURM_JOB_ID"
echo ""
printf "%0.s-" {1..10}
echo "${PATH}" | tr : \\n
} >> system_path.log

echo "Finished logging system PATH"

This creates a newline-delimited log of all the items listed in your system $PATH for your SLURM job. It's a nice record to have, especially in instances like this where something appears broken and is possibly related to system $PATH issues.

I'll add this somewhere to our Handbook...