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 ------------------------------------------------------------------------------ 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 Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
