Hi team, I am getting an error in nf-core/circRNA....
# circrna
g
Hi team, I am getting an error in nf-core/circRNA. Fatal LIMIT error: the number of junctions to be inserted on the fly =1054268 is larger than the limitSjdbInsertNsj=1000000 Fatal LIMIT error: the number of junctions to be inserted on the fly =1054268 is larger than the limitSjdbInsertNsj=1000000 SOLUTION: re-run with at least --limitSjdbInsertNsj 1054268 Where do I edit to allow to 1500000 as the limit. Am I able to add a params file? This is my bash nextflow run nf-core/circrna \ -profile conda \ -c custom.config \ -resume \ --input ADsample.csv \ --outdir /srv/scratch/grace/nextflow/AD_samples \ -r dev \ --tools ciriquant,circexplorer2,find_circ,circrna_finder \ --quantification_tools ciriquant,psirc,sum,max \ --gtf /srv/scratch/grace/gencode.v47.annotation.gtf \ --fasta /srv/scratch/grace/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \ --tools ciriquant,circexplorer2,find_circ,circrna_finder,mapsplice,dcc \
n
Hey, there is a pipeline parameter that you can use to set this limit. You can set this directly in the
nextflow run
command, or via a config file as described in the nextflow docs
g
Thank you!
Hi @Nico Trummer sorry to bother you again. I added --limitSjdbInsertNsj 1500000 to the pipeline and still getting an error. I made a my_params.yaml file and put --limitSjdbInsertNsj 1500000 in it and still getting same error.