Run denovotranscript on Klone

This entry describes running denovotranscript on the UW HPC Klone server. I generally followed the example workflow provided in the denovotranscript usage documentation.

It’s going to use the samplesheet.csv as input that was created by fetchngs

1. Run the pipeline with –qc_only with default params to check the quality of your reads.

# create a screen session
screen -S nextflow

# request a compute node (mem and time requests can be modified)
salloc -A srlab -p cpu-g2-mem2x -N 1 -c 1 --mem=16GB --time=12:00:00

# load the nextflow environment
mamba activate nextflow

# run nextflow pipeline
nextflow run \
nf-core/denovotranscript \
-resume \
-c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config \
--input /gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet.csv \
--outdir /gscratch/scrubbed/strigg/analyses/20240925_denovo \
--qc_only

This completed successfully

I looked at the multiqc and decided the first 10 bases should be trimmed from all reads. Example below

1. Run the pipeline with qc_only and any custom parameters that you have decided to use based on your data. Use resume to avoid unnecessarily rerunning unchanged steps. I next ran:

   nextflow run nf-core/denovotranscript \
   -c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config \
   --input /gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet.csv \
   --outdir /gscratch/scrubbed/strigg/analyses/20240925_denovo \
   --qc_only
   --extra_fastp_args='--trim_front1 10 --trim_front2 10' \
   --remove_ribo_rna \
   -resume
   

   this failed. I closed the screen with ctrl + A + D and then screen -XS nextflow quit

I decided to just try the whole pipeline and ran:

screen -S nextflow

salloc -A srlab -p cpu-g2-mem2x -N 1 -c 1 --mem=100GB --time=2-12:00:00

mamba activate nextflow

nextflow run nf-core/denovotranscript \
-c /gscratch/srlab/strigg/bin/uw_hyak_srlab.config \
--input /gscratch/scrubbed/strigg/analyses/20240925/samplesheet/samplesheet.csv \
--outdir /gscratch/scrubbed/strigg/analyses/20240925_denovo \
--extra_fastp_args='--trim_front1 10 --trim_front2 10' \
--remove_ribo_rna \
--busco_lineage= 'mollusca_odb10' \
-resume

Next time I would like to run the nextflow code with the following parameters:

-with-report nf_report
-with-trace
-with-timeline nf_timeline

Will see how far things get tomorrow.