beagle running error: Insufficient space for shared memory file

Question

[Shicheng Guo]

I want to phase the data (VCF) with beagle by the following command.

java -jar -Xmx32g beagle.16May19.351.jar gt=All_samples_Exome_QC.temp.vcf.recode.clean.chr19.vcf.recode.vcf ref=~/hpc/db/hg19/beagle/EUR/chr19.1kg.phase3.v5a.EUR.vcf.gz map=~/hpc/db/hg19/beagle/plink.chr19.GRCh37.map out=All_samples_Exome_QC.chr19.vcf

However, I received an error:

Java HotSpot(TM) 64-Bit Server VM warning: Insufficient space for shared memory file:
   32389
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

Error: unrecognized parameter: -Djava.io.tmpdir=./temp/

Any suggestion?

Thanks.

Answer 1

[h.mon]

You are splitting the -jar option from its argument beagle.16May19.351.jar. -Djava.io.tmpdir and -Xmx32g are arguments to the Java Virtual Machine, so it must come before the jar executable name. After -jar beagle.16May19.351.jar, must come the Beagle-specific options and arguments.

java -jar -Djava.io.tmpdir=./temp/ -Xmx32g beagle.16May19.351.jar \
  gt=All_samples_Exome_QC.temp.vcf.recode.clean.chr19.vcf.recode.vcf \
  ref=/gpfs/home/guosa/hpc/db/hg19/beagle/EUR/chr19.1kg.phase3.v5a.EUR.vcf.gz \
  map=/gpfs/home/guosa/hpc/db/hg19/beagle/plink.GRCh37.map.zip \
  out=All_samples_Exome_QC.chr19.vcf