This happened to me as well. I would have expected to see unpaired mates to end up in the unpaired.fastq file, instead it kills the process. Be aware, if you change validation_stringency to silent these reads will be ignored without any warning massage. Is there a way to change this behaviour.
Thanks > On Sep 3, 2014, at 1:21 PM, Joshua Gould <jgo...@broadinstitute.org> wrote: > > I'm trying to convert an aligned bam file (produced by the genomics > platform at the Broad) to a fastq file in order to perform alignment > against a custom genome. I get the error below. Do the fastq files > contain all the reads, except the ones for which a mate was not found? > Thanks. > Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM > validation error: ERROR: Found 13 unpaired mates > at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:465) > at picard.sam.SamToFastq.doWork(SamToFastq.java:192) > at > picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:183) > at picard.sam.SamToFastq.main(SamToFastq.java:137) > > ------------------------------------------------------------------------------ > Slashdot TV. > Video for Nerds. Stuff that matters. > http://tv.slashdot.org/ > _______________________________________________ > 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=164703151&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
