I want to use SortSam of picard to coordinate sort and index the individual WGS data (e.g. 73G). The memory size of one node in our cluster is near 126.2G. I even set the memory size in qsub command to 110G and distributed 100G to java, it still gave me the following error message : Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
What should I do ? Any advice will be appreciated.
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boymin2020 •
When writing SAM files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort a SAM file, and increases the amount of RAM needed. Default value: 500000. This option can be set to 'null' to clear the default value.
, it still gave me the following error message : Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException:
what @dariober said.
Use the standard option
TMP_DIR=
to change the default dir
java.io.IOException: No space left on device
I don't think the problem is with the memory but rather with the disk space. Picard writes temporary files to /tmp which usually is not a very large partition and it gets filled up easily. Try setting the TMP_DIR option to somewhere else, e.g. the current working directory (which is where samtools sort writes its tmp files).
For me, setting TMP_DIR (--TMP_DIR /home/tmp) didn't work in picard 2.21.1. What solved the issue was setting the environmental variable :
export _JAVA_OPTIONS=-Djava.io.tmpdir=/home/tmp .
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I have fixed the problem by adding the optional parameter
TMP_DIR. Thanks for help.