Picard FixMateInformation error?

[reeso123]

Hi all,

I am having some issues with picards FixMateInformation functions and was wondering if anyone has had similar problems. I have bam files which have been had duplicates marked using picard and local realignment around indels with GATK, but when I then follow with FixMateInformation it runs nicely for a while before I get the following error

Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:228)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:157)
at net.sf.picard.sam.FixMateInformation.writeAlignment(FixMateInformation.java:259)
at net.sf.picard.sam.FixMateInformation.doWork(FixMateInformation.java:181)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:175)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:118)
at net.sf.picard.sam.FixMateInformation.main(FixMateInformation.java:74)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.write(Native Method)
at org.xerial.snappy.SnappyOutputStream.writeInt(SnappyOutputStream.java:105)
at org.xerial.snappy.SnappyOutputStream.dump(SnappyOutputStream.java:126)
at org.xerial.snappy.SnappyOutputStream.flush(SnappyOutputStream.java:100)
at org.xerial.snappy.SnappyOutputStream.close(SnappyOutputStream.java:137)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:219)
... 7 more


No new fixed files result from this apart from empty temp files. I tried using samtools fix mate, and I thought it worked until I opened the new bams with IGV and noticed my reads were in red because the pairs are not mapped!

Any help with this would be much appreciated.
Many thanks,
Elliott

[Heisman]

When you have a question like this you should include the commands you used.

That said, it appears to say your problem is that you have no space left on device, so maybe it isn't specific to FixMates?

[Bukowski]

"No space left on device" - you've run out of disk space, or your allocation of it. Try having a look at the situation with 'df -h'. If you can redirect Picards temporary files somewhere else you might want to do that, if it appears you have enough disk space to store the output files.

[nans_bn]

similar error

Hello,

I am trying to run GATK local realignment and then the FixMateInformation with picard and got the same error
.....net.sf.picard.sam.FixMateInformation done....
Exception in thread "main" net.sf.samtools.util.RuntimeIOException: java.io.IOException: No space left on device...

I have more than enough same left on the device and I even tried to specify the temp folder
java -Xmx4g -jar FixMateInformation.jar \
INPUT=file.realigned.bam \
OUTPUT=file.realigned.fixedmateinfo.bam \
SO=coordinate \
VALIDATION_STRINGENCY=LENIENT \
CREATE_INDEX=true \
TMP_DIR=/"pwd"/temp

Any suggestions ?

Thank you.

[dGho]

thats weird
I had the same problem and specified a TMP_DIR like you did and it solved this issue for me. Are you sure you have enough mem? Are you trying to run this command along with other commands? I really don't know what the problem could be.

I have a suggestion that probably won't help but might be worth a try. You can specify more that one TMP_DIR. This could help depending on whether you are just running locally on ur pc, or have access to more memory.

considering this was posted in 2011, i am curious as to whether you found the solution to this problem for other user that may run into this issue

[nans_bn]

Hi,

Wow, that's a very very old post, .. what I did was use "MAX_RECORDS_IN_RAM=5000000" and then this command and this worked for me:
java -Xmx4g -jar FixMateInformation.jar \
INPUT=file.realigned.bam \
OUTPUT=file.realigned.fixedmateinfo.bam \
SO=coordinate \
MAX_RECORDS_IN_RAM=5000000 \
VALIDATION_STRINGENCY=LENIENT \
CREATE_INDEX=true \
TMP_DIR=$TMPDIR \

Cheers.