Hi, I am trying to use FastqToSam tool from Picard toolshed. But I keep getting the following exception:
Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollect
Though I have enough space on the disk. It seems some people have the same problem using Picard tools directly e.g. https://www.biostars.org/p/42613/
The problem was that the temp directory was filled up. The suggested solution was to make a folder called tmp in the current directory (mkdir tmp) and then run picard like this:
java -Xmx2g -Djava.io.tmpdir=pwd/tmp -jar SortSam.jar SORT_ORDER=coordinate INPUT=input.bam OUTPUT=output.sort TMP_DIR=pwd/tmp
Now my question is how can I implement the same solution in galaxy.
Many thanks.
Try to find the tool xml file and add the setting manually, you don't need to create the tmp folder though. The tool xml file is located somewhere in the shed_tools folder.