search

iraiosub / riboseq-flow

A Nextflow DSL2 pipeline to perform ribo-seq data analysis and comprehensive quality control.
MIT License
5 stars 1 forks source link

Genome index build memory issue #84

Closed mkatsanto closed 1 week ago

mkatsanto commented 2 weeks ago

Hello and thanks for the nice workflow! I am trying to execute riboseq-flow on some mouse data with the command nextflow run iraiosub/riboseq-flow -r v1.1.1 -profile singularity -resume --input samplesheet.csv --fasta /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/Mus_musculus.GRCm39.cdna.all.fa --gtf /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/Mus_musculus.GRCm39.112.gtf --contaminants_fasta /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/rRNA_mus_musculus.fasta --strandedness forward --skip_umi_extract

and got the error: EXITING because of FATAL PARAMETER ERROR: limitGenomeGenerateRAM=31000000000is too small for your genome SOLUTION: please specify --limitGenomeGenerateRAM not less than 81081488992 and make that much RAM available

Jun 13 16:08:15 ...... FATAL ERROR, exiting

Tried to adjust that with :

nextflow run iraiosub/riboseq-flow -r v1.1.1 -profile singularity -resume --input samplesheet.csv --fasta /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/Mus_musculus.GRCm39.cdna.all.fa --gtf /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/Mus_musculus.GRCm39.112.gtf --contaminants_fasta /scicore/home/zavolan/katsanto/PROJECTS/ribosome_profiling/riboseq_benchmark/ready_workflows/riboseq_pipeline/snakemake/annotation/rRNA_mus_musculus.fasta --strandedness forward --star_args limitGenomeGenerateRAM=81081488992 --skip_umi_extract

But it does not work. Is there any other option available I maybe missed?

Thanks

iraiosub commented 2 weeks ago

Hello Maria, thanks for trying our pipeline! The issue occurs because the fasta file provided contains sequences for all genes, rather than the chromosome sequences. riboseq-flow aligns to the genome, so you need to replace Mus_musculus.GRCm39.cdna.all.fa file with the corresponding one namedMus_musculus.GRCm39.dna.primary_assembly.fa.gz (you should be able to find it on the Ensembl 112 download page). That should fix it, let me know!

iraiosub commented 1 week ago

Hi Maria, any luck getting this to work? I will close the issue as solved for now. You are welcome to re-open if you're still encountering problems.

mkatsanto commented 1 week ago

Thank you for the help, yes I managed to get the workflow running.