Hi Dario,
You're totally right, I've made a bad copy paste! In that example,
picardtools worked, but when I use a bigger file (13gb), I get again the
error:
[Thu Feb 25 15:24:50 CET 2016] net.sf.picard.sam.SortSam
INPUT=Hs-Ang2Ba_S10_1.sam OUTPUT=Hs-Ang2Ba_S10_1.sort.bam
SORT_ORDER=coordinate VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
CREATE_MD5_FILE=false
INFO 2016-02-25 15:28:14 SortSam Read 10,000,000 records.
Elapsed time: 00:03:22s. Time for last 10,000,000: 202s. Last read
position: chr16:46,387,298
INFO 2016-02-25 15:31:29 SortSam Read 20,000,000 records.
Elapsed time: 00:06:37s. Time for last 10,000,000: 194s. Last read
position: chr16:18,677,422
[Thu Feb 25 15:32:40 CET 2016] net.sf.picard.sam.SortSam done. Elapsed
time: 7.83 minutes.
Runtime.totalMemory()=3712745472
To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
Exception in thread "main" net.sf.samtools.util.RuntimeIOException:
Problem writing temporary file
/tmp/root/sortingcollection.5612025169612768920.tmp. Try setting
TMP_DIR to a file system with lots of space.
at
net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:220)
at
net.sf.samtools.util.SortingCollection.add(SortingCollection.java:153)
at
net.sf.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:170)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:69)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at
net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.SortSam.main(SortSam.java:57)
Caused by: 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:160)
at net.sf.samtools.BAMRecordCodec.encode(BAMRecordCodec.java:37)
at
net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:213)
... 6 more
Caused by: java.io.IOException: No space left on device
at java.io.FileOutputStream.writeBytes(Native Method)
at java.io.FileOutputStream.write(FileOutputStream.java:300)
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)
... 10 more
Any idea?
Thank you again,
Giulia
On 25/02/2016 16:22, Dario Beraldi wrote:
Hi,
It doesn't look like an error to me, rather it's the usual info from
picard. Does output.sort.bam look sane? For example, can you index it
and does it have the same number of record as the input?
Dario
On 25 February 2016 at 14:27, Giulia <giulia.li...@ijm.fr
<mailto:giulia.li...@ijm.fr>> wrote:
Hi,
I'm trying to use Picard Tools (version 1.88 with java 1.6), but
for any
command that I tried (SortSam, ValideteSamFile, MarkDuplicates, etc) I
always got the same error:
java -Xmx8g -jar SortSam.jar I=input.sam O=output.sort.bam
SO=coordinate
VALIDATION_STRINGENCY=SILENT
[Thu Feb 25 14:27:44 CET 2016] net.sf.picard.sam.SortSam
INPUT=Hs-Ang2Bb_S11_2.sam OUTPUT=Hs-Ang2Bb_S11_2.sort.bam
SORT_ORDER=coordinate VALIDATION_STRINGENCY=SILENT VERBOSITY=INFO
QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000
CREATE_INDEX=false CREATE_MD5_FILE=false
INFO 2016-02-25 14:29:16 SortSam Finished reading inputs,
merging and writing to output now.
[Thu Feb 25 14:31:10 CET 2016] net.sf.picard.sam.SortSam done. Elapsed
time: 3.44 minutes.
Runtime.totalMemory()=3625779200
I couldn't find a solution for this error on internet, any idea of the
reasons?
Thank you for the help.
Giulia
--
Giulia Lizzo, PhD student
Institut Jacques Monod
Epigenome & Paleogenome Team
15, Rue Hélène Brion
75013 Paris
Tel. +33 157278131
NEW EMAIL giulia.li...@ijm.fr <mailto:giulia.li...@ijm.fr>
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Giulia Lizzo, PhD student
Institut Jacques Monod
Epigenome & Paleogenome Team
15, Rue Hélène Brion
75013 Paris
Tel. +33 157278131
NEW EMAIL giulia.li...@ijm.fr
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