Problem with running test of nf-core/rnaseq
Hello,
I was trying to run nf-core/rnaseq test for the 1st time. It stops half-way through with the following error after rounds of trials:
Error executing process > 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT'
Caused by:
Process `NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT` terminated with an error exit status (1)
Command executed:
bbsplit.sh \
-Xmx6g \
ref_primary=genome_gfp.fasta \
ref_sarscov2=GCA_009858895.3_ASM985889v3_genomic.200409.fna ref_human=chr22_23800000-23980000.fa \
path=bbsplit \
threads=2 \
build=1
cat <<-END_VERSIONS > versions.yml
"NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT":
bbmap: $(bbversion.sh 2>&1)
END_VERSIONS
Command exit status:
1
Command output:
Error occurred during initialization of VM
Could not reserve enough space for 6291456KB object heap
I don't know why it's like this and how to solve this issue so that I can proceed to analysis of my own datasets. I am running the workflow on HPC with memory of 50 G. Any response is greatly appreciated!
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If you are not trying separate reads from multiple genomes (e.g. PDX data) then you should use https://nf-co.re/rnaseq/parameters#skip_bbsplit option.
Best to ask in the nf-core slack https://nf-co.re/join in the rnaseq channel.