Setting temporary directory for GATK4 SortSam

Question

[Mehulsharma.253]

I used the SortSam option with GATK4 picard tools but it gives an error saying: htsjdk.samtools.util.RuntimeIOException: Problem writing temporary file file:///tmp/xxxxxx//sortingcollection.1885090825398510531.tmp. Try setting TMP_DIR to a file system with lots of space

I referred to this (Out Of Disk Space With Picard Tools ?) post with the following command:

java -Xmx2g -Djava.io.tmpdir=`pwd`/tmp -jar SortSam.jar SORT_ORDER=coordinate INPUT=input.bam OUTPUT=output.sort TMP_DIR=`pwd`/tmp

However, I run GATK directly from the Linux terminal with the command:

./gatk SortSam

Also, there is no SortSam.jar file in the directory. Only a gatk-package-4.0.11.0-local.jar.

How do I modify the syntax of the above command to set the temporary directory ?

[finswimmer]

Hello,

see A: Temporary Directory Problem in GATK4

fin swimmer

Answer 1

[Mehulsharma.253]

I got it using

 ./gatk --java-options "-Djava.io.tmpdir=/custom file path" SortSam -I=samplealn.sam -O=sortedsamplealn.bam -SO=coordinate --TMP_DIR=/custom file path