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:
Also, there is no SortSam.jar file in the directory. Only a gatk-package-18.104.22.168-local.jar.
How do I modify the syntax of the above command to set the temporary directory ?