Hello, I am running an nf-core/hic pipeline for breast samples (Tota

Remove duplicates execution process error about hic HOT 3 CLOSED

nf-core commented on May 26, 2024

Remove duplicates execution process error

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Comments (3)

nservant commented on May 26, 2024

Hi,
This is a memory issue.
You should increase the resource for this job.
By default, it is running with 12GB of RAM which seems to not be enough in your case.

I would suggest to create your own config file and to change the RAM for this process ;

process {
  withName:remove_duplicates {
    memory = 40.Gb
  }
}

see https://nf-co.re/usage/configuration#custom-configuration-files

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nservant commented on May 26, 2024

btw, what was the issue with v1.3.0 ? was it a conda issue ?

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koushik20 commented on May 26, 2024

Thank you for your suggestions the pipeline is successfully completed.

When running with version1.3.0 I am getting the following error

Execution cancelled -- Finishing pending tasks before exit
- Ignore this warning: params.schema_ignore_params = "saveReference,splitFastq" 
WARN: Found unexpected parameters:
* --saveReference: true
* --splitFastq: 10000000
Error executing process > 'bowtie2_end_to_end (HiChIP_MCF10A_R1)'

Caused by:
  Process exceeded running time limit (8h)

Command executed:

  INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
    bowtie2 --rg-id BMG --rg SM:HiChIP_MCF10A-A_S7_R1_001 \
  --very-sensitive --end-to-end --reorder \
  -p 4 \
  -x ${INDEX} \
  --un HiChIP_MCF10A-A_S7_R1_001_unmap.fastq \
  	-U HiChIP_MCF10A-A_S7_R1_001.fastq.gz | samtools view -F 4 -bS - > HiChIP_MCF10A-A_S7_R1_001.bam

Command exit status:
  -

Command output:
  (empty)

Work dir:
  /mnt/hichip_fastq/work/f9/f391d404fdf5768da48979b926096d

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

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