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Description
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
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System information
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