Hey Antonio,
could you run ValidateSamFile on the input BAM to MarkDuplicates? If you
have a small test case on which we can reproduce, please send it along,
N
On Mon, Nov 24, 2014 at 5:14 AM, antonio agraz <
antonio.agraz.bio...@gmail.com> wrote:
> Good afternoon. I send you this mail due to dubts using Picard.
>
> We use Picard/CleanSmar.jar:
> java -Xmx4g -jar $Picard_jarFolder/CleanSam.jar INPUT=$sample
> OUTPUT=$clean_picard VALIDATION_STRINGENCY=LENIENT 2>$log_clean_picard"
>
> Later we use fixmate a sort by samtools.
> but when we use the next step:
>
> java -Xmx2g -jar $Picard_jarFolder/MarkDuplicates.jar
> INPUT=$sorted1_samtools_bam OUTPUT=$sorted_picard_marked_bam TMP_DIR=./
> METRICS_FILE=$log_duplicate_metrics REMOVE_DUPLICATES=false
> ASSUME_SORTED=true VALIDATION_STRINGENCY=SILENT CREATE_INDEX=true
> 2>$log_picard_marked_bam"
>
> We have the next problem and we dont know why, if we had used CleanSam
> (which it is supposed to
>
> Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference
> alignments and setting MAPQ to 0 for unmapped reads)
>
> [Thu Nov 13 12:43:12 CET 2014] net.sf.picard.sam.MarkDuplicates done.
> Elapsed time: 10,13 minutes.
> Runtime.totalMemory()=1691418624
> Exception in thread "main" net.sf.samtools.SAMException: Exception when
> processing alignment for BAM index HS12_10750:8:2310:1400:98064#42 1/2 75b
> unmapped read.
> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:112)
> at net.sf.samtools
> .SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:168)
> at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:208)
> at net.sf.picard
> .cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
> at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:106)
> Caused by: net.sf.samtools.SAMException: Exception creating BAM index for
> record HS12_10750:8:2310:1400:98064#42 1/2 75b unmapped read.
> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:94)
> at net.sf.samtools.BAMFileWriter.writeAlignment(BAMFileWriter.java:109)
> ... 4 more
> Caused by: java.lang.ArrayIndexOutOfBoundsException: 8304
> at net.sf.samtools
> .BAMIndexer$BAMIndexBuilder.processAlignment(BAMIndexer.java:219)
> at net.sf.samtools.BAMIndexer.processAlignment(BAMIndexer.java:92)
> ... 5 more
>
> Previously, we have not reported this problem.
>
> Thanks. Best regards,
>
> Antonio M. Agraz
>
>
> ------------------------------------------------------------------------------
> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
> with Interactivity, Sharing, Native Excel Exports, App Integration & more
> Get technology previously reserved for billion-dollar corporations, FREE
>
> http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
> _______________________________________________
> Samtools-help mailing list
> Samtools-help@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/samtools-help
>
>
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
