Question: Out Of Disk Space With Picard Tools ?
6
gravatar for Gabriel R.
7.0 years ago by
Gabriel R.2.6k
Center for Geogenetik KĂžbenhavns Universitet
Gabriel R.2.6k wrote:

Hi, I am trying to run the following command:

java -Xmx2g -jar SortSam.jar SORT_ORDER=coordinate INPUT=input.bam OUTPUT=output.sort

But I keep getting: Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device Despite the fact that I have ample space to write.

Has anyone had similar trouble ?

picard tool • 16k views
ADD COMMENTlink modified 4 months ago by africainterpol1010 • written 7.0 years ago by Gabriel R.2.6k
5

perhaps it is using the temporary directory that is located on a different, smaller partition,

ADD REPLYlink written 7.0 years ago by Istvan Albert ♦♦ 80k
28
gravatar for John St. John
7.0 years ago by
John St. John1.1k
San Francisco, CA, Cancer Therapeutics Innovation Group
John St. John1.1k wrote:

That sounds like an issue with your system's TMP directory filling up. Why not make a folder called tmp in your current directory (mkdir tmp) where you are doing your work 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

It is possible that this part:

TMP_DIR=`pwd`/tmp

would be sufficient, but setting -Djava.io.tmpdir=bla should work for java programs in general.

ADD COMMENTlink written 7.0 years ago by John St. John1.1k

Worked ! Many thanks !

ADD REPLYlink written 7.0 years ago by Gabriel R.2.6k

Thanks.. worked for me as well.

ADD REPLYlink written 6.8 years ago by Sudeep1.6k

that solved the no-space issue, but now I am getting this: Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.FileNotFoundException: /Picard/picard-tools-1.72/pwd/tmp/sortingcollection.4875296484959495534.tmp (Too many open files) Anyone had similar issue?

ADD REPLYlink written 6.6 years ago by sjohn20
1

Add the parameter named MAX_FILE_HANDLES_FOR_READ_ENDS_MAP, I set it to 1000 and it helped :-) with the explanation here

ADD REPLYlink modified 6.5 years ago by Istvan Albert ♦♦ 80k • written 6.5 years ago by Biomonika (Noolean)3.0k

You have to go to /etc/security/limits.conf and put it like this:

#<domain>      <type>  <item>         <value>
#
*               hard    nofile            65536
*               soft    nofile            65536

then you can have 65536 open files at the same time with your user. You will need root rights.

ADD REPLYlink modified 6.6 years ago by Istvan Albert ♦♦ 80k • written 6.6 years ago by roalva180

Didn't work for me. I run picard via GATK 4.0.11.

I made a tmp folder in my GATK directory and used the command:

./gatk SortSam -I=/home/xxxxx/Desktop/folder/input.sam -O=/home/xxxxx/Desktop/folder/sortedsample.bam -SO=coordinate TMP_DIR=`pwd`/tmp

Got the error:

Invalid argument 'TMP_DIR=tmp'.

ADD REPLYlink written 4 months ago by Mehulsharma.25310

TMP_DIR is not a part of the command, it's an environmental variable

ADD REPLYlink written 4 months ago by WouterDeCoster38k
1
gravatar for Mehulsharma.253
4 months ago by
Mehulsharma.25310 wrote:

The problem is, as others said with a probable low space in the default temporary directory. I changed my directory to a custom one. Worked perfectly for me using this code:

./gatk --java-options "-Djava.io.tmpdir=/custom file path" SortSam -I=samplealn.sam -O=sortedsamplealn.bam -SO=coordinate --TMP_DIR=/custom file path
ADD COMMENTlink written 4 months ago by Mehulsharma.25310
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