Problem with running test of nf-core/rnaseq
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Entering edit mode
4 months ago
Deepblue ▴ 10

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!

nf-core • 263 views
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Entering edit mode

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.

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Best to ask in the nf-core slack https://nf-co.re/join in the rnaseq channel.

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