Hey Jasleen,
"unpaired" in this context means that we do not expect that the read has a
pair (the pair bit in the flag is unset). It looks like you have a read
that is paired, but its mate is not in the example.bam. You should fix up
your input BAM file to make it work without validation errors,
N
On Fri, Feb 27, 2015 at 8:06 PM, Jasleen Grewal <jk...@sfu.ca> wrote:
> Hi Samtools Support,
>
> I am currently testing out Picard Tools 1.119’s release of SamToFastq.jar.
> From my understanding of the user guide, this release should allow for
> three different fastq outputs from a paired bam input (two fastq’s for the
> paired reads and a third for unpaired ones). However, trying this on a test
> bam with a known unpaired read, I get the first two outputs but the
> unpaired_fastq is always unpopulated and the SAM validation error about
> unpaired mates shows up. Has this option not been fully implemented yet or
> is there any additional flag I am missing?
> *Current command:*
> > java -Xmx4g -jar /path/to/picardtools/SamToFastq.jar INPUT=example.BAM
> FASTQ=test1.fq SECOND_END_FASTQ=test2.fq UNPAIRED_FASTQ=test3.fq
>
> *Runtime output*
> picard.sam.SamToFastq INPUT=exampleBAM.bam FASTQ=test1.fq
> SECOND_END_FASTQ=test2.fq UNPAIRED_FASTQ=test3.fq OUTPUT_PER_RG=false
> RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false READ1_TRIM=0
> READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO
> QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5
> MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false
> [Fri Feb 27 16:57:04 PST 2015] Executing as jgre...@xhost09.bcgsc.ca on
> Linux 2.6.18-194.3.1.el5 amd64; Java HotSpot(TM) 64-Bit Server VM
> 1.7.0_13-b20; Picard version:
> 1.119(d44cdb51745f5e8075c826430a39d8a61f1dd832_1408991805) IntelDeflater
> [Fri Feb 27 16:57:05 PST 2015] picard.sam.SamToFastq done. Elapsed time:
> 0.00 minutes.
> Runtime.totalMemory()=996343808
> To get help, see http://picard.sourceforge.net/index.shtml#GettingHelp
> Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM
> validation error: ERROR: Found 1 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)
>
> Resultant file sizes are as expected for test1.fq and test2.fq, but 0 for
> test3.fq.
>
> Any help with this would be appreciated!
>
> Cheers,
> Jasleen.
>
>
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