Hi I am not too sure what to make of this.
the sam file was from bwa
is it a bug in bwa output?
java -Xmx2g -jar /home/corona/bin/source/picard-tools-1.14/ViewSam.jar INPUT=sorted.sam ALIGNMENT_STATUS=Aligned > sortedaligned.sam
Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. MAPQ must should be 0 for unmapped read.; File sorted.sam; Line 8910023
Line: ./S2:747_1696_219 4 chr18 90771994 25 48M * 0 0 AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGTTTGGGGCTT ]]]]]]PLQ]]XW[]QA6H]]VI+3]M9FSIFG@QQ:!)]0+OJRL:7 XT:A:U CM:i:1 XN:i:10 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:40C7
at net.sf.samtools.SAMTextReader.reportErrorParsingLine(SAMTextReader.java:176)
at net.sf.samtools.SAMTextReader.access$500(SAMTextReader.java:40)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:385)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:232)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:196)
at net.sf.picard.sam.ViewSam.doWork(ViewSam.java:68)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.ViewSam.main(ViewSam.java:58)
the sam file was from bwa
is it a bug in bwa output?
java -Xmx2g -jar /home/corona/bin/source/picard-tools-1.14/ViewSam.jar INPUT=sorted.sam ALIGNMENT_STATUS=Aligned > sortedaligned.sam
Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. MAPQ must should be 0 for unmapped read.; File sorted.sam; Line 8910023
Line: ./S2:747_1696_219 4 chr18 90771994 25 48M * 0 0 AGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGGGTTAGTTTGGGGCTT ]]]]]]PLQ]]XW[]QA6H]]VI+3]M9FSIFG@QQ:!)]0+OJRL:7 XT:A:U CM:i:1 XN:i:10 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:40C7
at net.sf.samtools.SAMTextReader.reportErrorParsingLine(SAMTextReader.java:176)
at net.sf.samtools.SAMTextReader.access$500(SAMTextReader.java:40)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:385)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:232)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:196)
at net.sf.picard.sam.ViewSam.doWork(ViewSam.java:68)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143)
at net.sf.picard.sam.ViewSam.main(ViewSam.java:58)
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