Thank you both for the advice, I changed the temporary directory and it
works now.
Thanks again for your help and explanations.
Giulia
On 25/02/2016 16:48, Dario Beraldi wrote:
On 25 February 2016 at 15:43, Andrew Bjonnes
<bjon...@broadinstitute.org <mailto:bjon...@broadinstitute.org>> wrote:
It seems you have issues writing to the default temp directory.
You can specify a directory to use as the temp dir with
picardtools with the TMP_DIR variable:
https://broadinstitute.github.io/picard/command-line-overview.html .
Try setting this to a new temp directory in your workspace.
I was going to said that... /tmp is usually not very large.
Andrew
On Thu, Feb 25, 2016 at 10:35 AM Giulia <giulia.li...@ijm.fr
<mailto:giulia.li...@ijm.fr>> wrote:
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
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Institut Jacques Monod
Epigenome & Paleogenome Team
15, Rue Hélène Brion
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Institut Jacques Monod
Epigenome & Paleogenome Team
15, Rue Hélène Brion
75013 Paris
Tel. +33 157278131
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