Can Trimmomatic be skipped while running Wochenende ?

[arpit20328]

Hi

So after all settings in config.yml

I ran

python3 run_Wochenende.py arpit_R1.fastq --aligner bwamem --readType PE --metagenome 2021_12_meta_fungi_human_masked --threads 144 --no_abra --remove_mismatching 3 --no_fastqc

can I stop Trimmomatic ? I have already removed adapters etc.

Please note I am not using nf or slurm. I am just executing python scripts.

[colindaven]

Hi Arpit, I don't think you can turn off trimmomatic. We always ran it from raw sequence to avoid saving the trimmed.

I can also advise you to use max 24 threads for performance reasons (there are minimal gains after 20-24 threads for almost all tools). If you're lucky enough to have a big machine, just start six or seven python processes in parallel using this system, or multiple shells.

python3 run_Wochenende.py args &
python3 run_Wochenende.py args &
python3 run_Wochenende.py args &
python3 run_Wochenende.py args &

[colindaven]

That said, you can also comment out Lines 1541 -48 in the python script and see if that works for you (assuming paired end PE reads, there is a different section for single ended SE reads).

Wochenende/run_Wochenende.py

Line 1541 in 0eed8da

if args.nextera:

[arpit20328]

@colindaven will try

[arpit20328]

@colindaven yes trimming stopped after commenting 1541 to 1548 lines . thanks