Movatterモバイル変換


[0]ホーム

URL:


Skip to content

Navigation Menu

Sign in
Appearance settings

Search code, repositories, users, issues, pull requests...

Provide feedback

We read every piece of feedback, and take your input very seriously.

Saved searches

Use saved searches to filter your results more quickly

Sign up
Appearance settings

Out of memory error in MAKE_COMPATIBLE:PLINK2_VCF step when processing Illumina WGS gVCF-derived VCF #448

Open
Labels
bugSomething isn't working
@Janeyre91

Description

@Janeyre91

Description of the bug

I'm running pgsc_calc on a Illumina WGS (on a server with 1TB of RAM). The WGS was produced using Haplotype caller (gVCF mode) followed by GenotypeGVCFs:
java -jar /home/tools/gatk-4.6.2.0/gatk-package-4.6.2.0-local.jar GenotypeGVCFs -R Homo_sapiens_assembly38_noalt.fasta -V X2121.snps.raw.g.vcf.gz -O X2121.raw.vcf.gz --dbsnp dbSNP155_fixed.vcf.gz --include-non-variant-sites true

The command that I've used for pgsc_calc is:
nextflow run pgscatalog/pgsc_calc \ -profile docker \ --input samplesheet.csv \ --pgs_id PGS001931 \ --efo_id EFO_0009695 \ --target_build GRCh38 \ --liftover \ --hg19_chain https://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/hg19ToHg38.over.chain.gz \ --hg38_chain https://hgdownload.soe.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz \ --run-ancestry https://ftp.ebi.ac.uk/pub/databases/spot/pgs/resources/pgsc_HGDP+1kGP_v1.tar.zst \ -c custom.config
My custom.config is:
`process {
executor = 'local'

withName: 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF' {    memory = '300.GB'    cpus = 16    time = '48.h'}

}`
I'm obtaining this error:

`ERROR ~ Error executing process > 'PGSCATALOG_PGSCCALC:PGSCCALC:MAKE_COMPATIBLE:PLINK2_VCF (X2121 chromosome ALL)'

Caused by:
Process terminated with an error exit status (2)

Command executed:

plink2
--threads 16
--memory 307200
--set-all-var-ids '@:#:$r:$a'
--max-alleles 2
--freq
--missing vcols=fmissdosage,fmiss
--new-id-max-allele-len 100 missing
--vcf X2121.raw.vcf
--allow-extra-chr --chr 1-22, X, Y, XY
--make-pgen vzs pvar-cols="-xheader,-maybequal,-maybefilter,-maybeinfo,-maybecm"
--out GRCh38_X2121_ALL

Command exit status: 2

Output:
Out of memory.`

Thanks in advance!!!

Command used and terminal output

Relevant files

No response

System information

No response

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugSomething isn't working

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions


      [8]ページ先頭

      ©2009-2025 Movatter.jp