qualimap rnaseq error

[Him26]

Hi I am trying to run qualimap rnaseq and I get the following error

Failed to run rnaseq
net.sf.samtools.util.RuntimeIOException: Write error; BinaryCodec in writemode; streamed file (filename not available)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:199)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:189)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:139)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:210)
at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:150)
at net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.sortSamByName(ComputeCountsTask.java:143)
at org.bioinfo.ngs.qc.qualimap.process.ComputeCountsTask.run(ComputeCountsTask.java:429)
at org.bioinfo.ngs.qc.qualimap.process.RNASeqQCAnalysis.run(RNASeqQCAnalysis.java:68)
at org.bioinfo.ngs.qc.qualimap.main.RnaSeqQcTool.execute(RnaSeqQcTool.java:188)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool.run(NgsSmartTool.java:187)
at org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain.main(NgsSmartMain.java:111)
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:318)
at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:126)
at net.sf.samtools.util.BinaryCodec.writeBytes(BinaryCodec.java:197)
... 12 more

I have plenty of space but why am I getting IOException?

following is the output from the run I did
Java memory size is set to 6G
Launching application...

QualiMap v.2.2-dev
Built on 2015-12-08 14:47

Selected tool: rnaseq
Mon Feb 22 21:41:33 KST 2016 WARNING Output folder already exists, the results will be saved there

Mon Feb 22 21:41:33 KST 2016 WARNING the directory used to write counts will be the output dir

Initializing regions from /genecode/gencode.v12.annotation.gtf...

Initialized 100000 regions...
Initialized 200000 regions...
Initialized 300000 regions...
Initialized 400000 regions...
Initialized 500000 regions...
Initialized 600000 regions...
Initialized 700000 regions...
Initialized 800000 regions...
Initialized 900000 regions...
Initialized 1000000 regions...
Initialized 1100000 regions...
Initialized 1200000 regions...
Initialized 1300000 regions...
Initialized 1400000 regions...
Initialized 1500000 regions...
Initialized 1600000 regions...
Initialized 1700000 regions...
Initialized 1800000 regions...
Initialized 1900000 regions...
Initialized 2000000 regions...
Initialized 2100000 regions...
Initialized 2200000 regions...
Initialized 2300000 regions...
Initialized 2400000 regions...
Initialized 2500000 regions...
Initialized 2600000 regions...

Initialized 2616297 regions it total

Starting constructing transcripts for RNA-seq stats...
Finished constructing transcripts

Starting BAM file analysis

Sorting BAM file by name...

Read 10000000 records.
Read 20000000 records.
Read 30000000 records.
Read 40000000 records.
Mon Feb 22 21:51:19 KST 2016

[GenoMax]

Have you tried increasing the RAM allocation to 16G?

[Him26]

I've tried to increase the memory to 48G and still get the same error...
is there another reason for this?

[GenoMax]

Other error you can investigate is this one:

Caused by: java.io.IOException: No space left on device

Is /tmp or some other storage device filling-up/reaching quota?

[vasisht]

Try setting the java tmp dir using JAVA_OPTS shell variable that's picked up by qualimap.

e.g. export JAVA_OPTS="-Djava.io.tmpdir=/scratch -Xmx10G"

Qualimap creates temporary bam files when sorting by name, which take up space in the system tmp dir (usually /tmp). You can also avoid this by sorting the bam file by name before running Qualimap.