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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