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hoelzer-lab / rnaflow

A simple RNA-Seq differential gene expression pipeline using Nextflow
GNU General Public License v3.0
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ERROR ~ Error executing process > 'download_sortmerna:sortmernaGet' #219

Open apkbala107 opened 1 year ago

apkbala107 commented 1 year ago

ERROR ~ Error executing process > 'download_sortmerna:sortmernaGet'

Caused by: Process requirement exceeds available CPUs -- req: 24; avail: 16

Command executed:

git clone https://github.com/biocore/sortmerna.git indexdb_rna --ref ./sortmerna/data/rRNA_databases/silva-bac-16s-id90.fasta,./sortmerna/data/rRNA_databases/silva-bac-16s-id90:./sortmerna/data/rRNA_databases/silva-bac-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-bac-23s-id98:./sortmerna/data/rRNA_databases/silva-arc-16s-id95.fasta,./sortmerna/data/rRNA_databases/silva-arc-16s-id95:./sortmerna/data/rRNA_databases/silva-arc-23s-id98.fasta,./sortmerna/data/rRNA_databases/silva-arc-23s-id98:./sortmerna/data/rRNA_databases/silva-euk-18s-id95.fasta,./sortmerna/data/rRNA_databases/silva-euk-18s-id95:./sortmerna/data/rRNA_databases/silva-euk-28s-id98.fasta,./sortmerna/data/rRNA_databases/silva-euk-28s-id98:./sortmerna/data/rRNA_databases/rfam-5s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5s-database-id98:./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98.fasta,./sortmerna/data/rRNA_databases/rfam-5.8s-database-id98 -v mv sortmerna/data/rRNA_databases . tar zcvf rRNA_databases.tar.gz rRNA_databases rm -r rRNA_databases rm -r sortmerna

Command exit status:

Command output: (empty)

Work dir: /workspace/rnaflow/work/87/8721d1843429a166cadcfb325bb6bb

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details WARN: Failed to render execution report -- see the log file for details WARN: Failed to render execution timeline -- see the log file for details

hoelzer commented 1 year ago

hey @apkbala107 !

Can you please provide the used nextflow run ... command?

I guess you are running the pipeline on a cluster machine? If so, the default CPU number for SortMeRNA is configured to be 24:

https://github.com/hoelzer-lab/rnaflow/blob/master/configs/nodes.config#L7

If you don't have that many resources, try running the pipeline with the local profile and configure the number of CPUs per process and the maximum number of used CPUs via the respective parameters.

Another way would be, to clone the code from the repository, change the CPU number in the nodes.config file, and then run via

nextflow run rnaflow/main.nf ...