ERROR ~ Error executing process > 'download_sortmerna:sortmernaGet'

[apkbala107]

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]

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 ...