picard SamToFastq error in umapped reads which MAPQ is not 0

[upper]

Set the VALIDATION_STRINGENCY to LENIENT. Picard will still warn you about those reads, but it will go past them.

bwa will throw the 4 flag if a read hangs off the edge of one of your references, but it will also give it a mapping position and MAPQ. That likely is the source of your problem reads.

thank you,picard ignore these reads and continue process,and also picard just report error as before but didnot remove these reads,this is what I want.

INPUT=s_3_2/s_3_2_unmap_genome.sam FASTQ=s_3_2/s_3_2_unmap_genome.fq VALIDATION_STRINGENCY=LENIENT

Ignoring SAM validation error due to lenient parsing:
Error parsing text SAM file. MAPQ should be 0 for unmapped read.; Line 3205583
Line: HWUSI-EAS724_0039:3:34:15714:3092#0       20      9       124595110       37      80M     *       0       0       AGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAA
ATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGG        hggh]hghhhghghhhhhghhhhhhhhhhhdhhhhhhhcfhhghhhhhhhchhhghhfdhhhghhhhhhgghhghhghhh        XT:A:U  NM:i:1  XN
:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:0G79

[swbarnes2]

Set the VALIDATION_STRINGENCY to LENIENT. Picard will still warn you about those reads, but it will go past them.

bwa will throw the 4 flag if a read hangs off the edge of one of your references, but it will also give it a mapping position and MAPQ. That likely is the source of your problem reads.

[upper]

Hi,
SamToFastq.jar will be stop when it meet the unmapped reads which flag is 4 or 20 but the MAPQ is not 0. Picard is not so smart,it couldnot skip this reads but stop to deal next reads.
I am also confused why unmapped reads MAPQ is not 0? I found many of unmapped reads which flag is 4 or 20 has MAPQ and OPT column. MAPQ 37 is the highest sore in bwa reasult and normal means its unique mapping reads.
I use bwa Version: 0.6.1-r104 to do mapping.
Can someone know how to deal these reads,I want to mapping unmaped reads to junction？

java -jar SamToFastq.jar INPUT=s_3_2_unmap_genome.sam FASTQ=s_3_2_unmap_genome.fq


Wed Dec 05 09:27:59 HKT 2012] net.sf.picard.sam.SamToFastq done. Elapsed time: 1.19 minutes.
Runtime.totalMemory()=262864896
FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. MAPQ should be 0 for unmapped read.; Line 3205583
Line: HWUSI-EAS724_0039:3:34:15714:3092#0       20      9       124595110       37      80M     *       0       0       AGTTAATGTAGCTTAATAACAAAGCAAAGCACTGAAA
ATGCTTAGATGGATAATTGTATCCCATAAACACAAAGGTTTGG        hggh]hghhhghghhhhhghhhhhhhhhhhdhhhhhhhcfhhghhhhhhhchhhghhfdhhhghhhhhhgghhghhghhh        XT:A:U  NM:i:1  XN
:i:1  X0:i:1  X1:i:0  XM:i:1  XO:i:0  XG:i:0  MD:Z:0G79
        at net.sf.samtools.SAMTextReader.reportErrorParsingLine(SAMTextReader.java:230)
        at net.sf.samtools.SAMTextReader.access$500(SAMTextReader.java:40)
        at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:434)
        at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:278)
        at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:250)
        at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:641)
        at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:619)
        at net.sf.picard.sam.SamToFastq.doWork(SamToFastq.java:129)
        at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
        at net.sf.picard.sam.SamToFastq.main(SamToFastq.java:118)