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Re: [Samtools-help] picard tools error
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From: Giulia <giu...@ij...> - 2016-02-25 16:18:38
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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 > <bj...@br... <mailto:bj...@br...>> 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 <giu...@ij... > <mailto:giu...@ij...>> 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 <giu...@ij... >> <mailto:giu...@ij...>> 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 <tel:%2B33%20157278131> >> NEW EMAIL giu...@ij... <mailto:giu...@ij...> >> >> >> ------------------------------------------------------------------------------ >> 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! >> http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 >> _______________________________________________ >> Samtools-help mailing list >> Sam...@li... >> <mailto:Sam...@li...> >> https://lists.sourceforge.net/lists/listinfo/samtools-help >> >> > > -- > Giulia Lizzo, PhD student > Institut Jacques Monod > Epigenome & Paleogenome Team > 15, Rue Hélène Brion > 75013 Paris > > Tel.+33 157278131 <tel:%2B33%20157278131> > NEW EMA...@ij... <mailto:giu...@ij...> > > ------------------------------------------------------------------------------ > 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! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140_______________________________________________ > Samtools-help mailing list > Sam...@li... > <mailto:Sam...@li...> > https://lists.sourceforge.net/lists/listinfo/samtools-help > > -- Giulia Lizzo, PhD student Institut Jacques Monod Epigenome & Paleogenome Team 15, Rue Hélène Brion 75013 Paris Tel. +33 157278131 NEW EMAIL giu...@ij... |
