Trim galore gets stuck on quality and adapter trimming

[aman-akash]

Hey,

I am trying to trim pacbio sequencing data in a fastq file using trim galore. However, in every run trim galore gets stuck on the trimming step and never goes to the next step. I can see the trimmed file is created and has a relevant size as well.
When I checked the run status I saw that the trim galore job had been suspended for over a day.

Any help regarding this would be great. Thank you for making a nice tool.

Cheers,
Aman

Command :
trim_galore -q 7 --fastqc --length 1000 -j 4 -o trimmed ../SRR16*****.fastq

I am also attaching the report generated.

SUMMARISING RUN PARAMETERS
==========================
Input filename: ../SRR16******.fastq
Trimming mode: single-end
Trim Galore version: 0.6.10
Cutadapt version: 4.5
Python version: could not detect
Number of cores used for trimming: 4
Quality Phred score cutoff: 7
Quality encoding type selected: ASCII+33
Using Nextera adapter for trimming (count: 468). Second best hit was smallRNA (count: 329)
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length before a sequence gets removed: 1000 bp
Running FastQC on the data once trimming has completed

[FelixKrueger]

I am not sure I can be of great help here as I have never tried to trim PacBio reads before. Trim Galore is specifically meant to be a short-read trimmer with a focus on Illumina read data. I am not sure if Cutadapt itself is capable of trimming PacBio reads, but maybe there is software out there that is specifically designed to work with it?

[aman-akash]

Read that it worked for some people even with pacbio reads.

Thanks for the clarification.

Cheers.

[FelixKrueger]

hmm, maybe it does work but it just takes a long time? I would probably first try it out with a small subset to see if it works in principle, and if it does through some more parallel compute power at it (via -j). Just monitor the system performance (e.g via top) to make sure that it is still running....