Open rrlove-cdc opened 7 months ago
@rrlove-cdc Did you solve this problem? I run into the same bug as yours in NFCORE_SAREK:SAREK:FASTQC
. I will be grateful if you share information. Thanks.
[nf-core/sarek] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_SAREK:SAREK:FASTQC (test-test_L2)'
Caused by:
Process `NFCORE_SAREK:SAREK:FASTQC (test-test_L2)` terminated with an error exit status (1)
Command executed:
printf "%s %s\n" test_1.fastq.gz test-test_L2_1.gz test_2.fastq.gz test-test_L2_2.gz | while read old_name new_name; do
[ -f "${new_name}" ] || ln -s $old_name $new_name
done
fastqc \
--quiet \
--threads 2 \
--memory 6656 \
test-test_L2_1.gz test-test_L2_2.gz
cat <<-END_VERSIONS > versions.yml
"NFCORE_SAREK:SAREK:FASTQC":
fastqc: $( fastqc --version | sed '/FastQC v/!d; s/.*v//' )
END_VERSIONS
Command exit status:
1
Command output:
Error occurred during initialization of VM
Could not reserve enough space for 13631488KB object heap
Command wrapper:
Error occurred during initialization of VM
Could not reserve enough space for 13631488KB object heap
Description of the bug
The sarek pipeline repeatedly errors out at the GATK MarkDuplicates step with the message:
"Error occurred during initialization of VM Could not reserve enough space for 50331648KB object heap"
Sometimes an error message for "FASTQ_ALIGN_BWAMEM_MEM2_DRAGMAP_SENTIEON:BWAMEM1_MEM" also appears.
With help from our HPC support team, I have tried:
In all cases, GATK still tries to request a larger heap size, so the custom settings don't seem to be getting passed to the program. A member of the HPC support team suggested the issue might be solvable by adding 'ext.args = "-Xmx8g"' in the module-level config files rather than the user-level config file.
Command used and terminal output
Relevant files
nextflow.log.zip sarek_test.zip
System information
Nextflow version 23.04.1, nf-core/sarek v3.3.2-gf034b73 HPC + singularity on SGE CentOS