FastQC fails after trimming due to "No such file or directory..."

[kubu4]

We ran TrimGalore, combined with FastQC arguments. However, each FastQC step failed in a fashion like this:

RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.fq.gz
=============================================
162780101 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz
file_1: zr3616_1_R1_trimmed.fq.gz, file_2: zr3616_1_R2_trimmed.fq.gz

>>>>> Now validing the length of the 2 paired-end infiles: zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz <<<<<
Writing validated paired-end Read 1 reads to zr3616_1_R1_val_1.fq.gz
Writing validated paired-end Read 2 reads to zr3616_1_R2_val_2.fq.gz

Total number of sequences analysed: 162780101

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1543746 (0.95%)

  >>> Now running FastQC on the validated data zr3616_1_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 651120404.

  >>> Now running FastQC on the validated data zr3616_1_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 651120404.
Deleting both intermediate output files zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz

We're not really sure how to address this. We've confirmed the validated files exist, so they're present. Would you happen to have any ideas/suggestions?

---

Program version info, if that helps:

Multicore support not enabled. Proceeding with single-core trimming.
Path to Cutadapt set as: '/usr/lusers/yaaminiv/.local/bin/cutadapt' (user defined)
Cutadapt seems to be working fine (tested command '/usr/lusers/yaaminiv/.local/bin/cutadapt --version')
Cutadapt version: 3.1
single-core operation.
No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Output will be written into the directory: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/
Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.6.6

[FelixKrueger]

The relevant error message is: Can't exec "fastqc". If you want to run FastQC as part of Trim Galore, you need to download and install it first. If you can type:

fastqc --help

on the command line and see the FastQC help text, then it will also work within Trim Galore. In effect it just executes

fastqc zr3616_1_R1_val_1.fq.gz zr3616_1_R2_val_2.fq.gz

for you once the trimming is complete. Does that make sense?

[kubu4]

Does that make sense?

Definitely! Thanks for the quick response!

I'll take this up with my colleague who was having difficulty. They had successfully run TrimGalore the day before (with the identical command - just different list of FastQs) without issue. I'll double-check with them to see if they did something to accidentally remove FastQC from their system $PATH.