On 25 February 2016 at 15:43, Andrew Bjonnes <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> 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> 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
>>>
>>>
>>>
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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
>>
>>
>> ------------------------------------------------------------------------------
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month
>> Monitor end-to-end web transactions and take corrective actions now
>> Troubleshoot faster and improve end-user experience. Signup Now!
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>
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