Question: Out Of Disk Space with Picard's FastqtoSam Tools from Galaxy
0
gravatar for mainulhossain
7 months ago by
mainulhossain0 wrote:

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.

samtools galaxy picard • 300 views
ADD COMMENTlink modified 7 months ago by Bjoern Gruening5.1k • written 7 months ago by mainulhossain0
1

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.

ADD REPLYlink modified 7 months ago • written 7 months ago by oskar10
2
gravatar for Bjoern Gruening
7 months ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

I think a better way is to set this as part of the job_conf and point it to a fast, local, big scratch space. For example you can export _JAVA_OPTIONS=" -XX:MaxPermSize=2G -Xmx8G -Xms1G -Djava.io.tmpdir=/data/2/galaxy_db/tmp" or set it as variable in your job_conf.xml file like here .

Hope that helps, Bjoern

ADD COMMENTlink modified 7 months ago • written 7 months ago by Bjoern Gruening5.1k
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