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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