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Help with samtools problem "Error parsing text SAM file. MAPQ should be 0 for unmapped read"?

kshorttkshortt Member
edited August 2016 in Ask the GATK team

Hello, I am trying to convert a sam file to bam and am getting the below error. Can you help me with how I can fix this?

Exception in thread "main" net.sf.samtools.SAMFormatException: Error parsing text SAM file. MAPQ should be 0 for unmapped read.; Line 30415
Line: SNL160:121:HNWM3BCXX:2:1103:5604:21129_1 4 chrM 16071 37 233M1D13M * 0 0 TACCAAATTTTAACTCTCCAAACCCCCCACCCCCTCCTCTTAATGCCAAACCCCAAAAACACTAAGAACTTGAAAGACATATAATATTAACTATCAAACCCTATGTCCTGATCAA
TTCTAGTAGTTCCCAAAATATGACTTATATTTTAGTACTTGTAAAAATTTTACAAAATCATGTTCCGTGAACCAAAACTCTAATCATACTCTATTACGCAATAAACATTAACAAGTTAATGTAGCTTAATA DDDDDIHIIIIIIIIIIIIIIIIIIIIIIIIIIIIHIIIIIIIIIIIIHIEHHIHIIIIHEHHIIIIGHIHIIIGIHIHIIIIIIIIIIIHHIIGHHIH
IIHHIIIIIIIIIIIIHIHHHIIIIIIIIIIHIIII[email protected]?GGHGFHHGIIIH.@EHIIHHCHEHEHCHEB.BHEFEHIH.FHH..A XT:A:N NM:i:9 XN:i:18 X0:i:1 X1:i:0 XM:i:8 XO:i:1 XG:i:1 MD:Z:229A3^C2C1C1G0
G0A0G2C0
at net.sf.samtools.SAMLineParser.reportErrorParsingLine(SAMLineParser.java:427)
at net.sf.samtools.SAMLineParser.parseLine(SAMLineParser.java:331)
at net.sf.samtools.SAMTextReader$RecordIterator.parseLine(SAMTextReader.java:237)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:225)
at net.sf.samtools.SAMTextReader$RecordIterator.next(SAMTextReader.java:201)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:672)
at net.sf.samtools.SAMFileReader$AssertableIterator.next(SAMFileReader.java:650)
at net.sf.picard.sam.SortSam.doWork(SortSam.java:68)
at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
at net.sf.picard.sam.SortSam.main(SortSam.java:57)
"

Edit: I ran ValidateSamFile and obtained the following output:

ValidateSamFile1_ks_18423.out

HISTOGRAM java.lang.String

Error Type Count
ERROR:INVALID_MAPPING_QUALITY 26
ERROR:MISSING_READ_GROUP 1
WARNING:RECORD_MISSING_READ_GROUP 1864385

What do I need to do to correct these errors in the sam file and how can I avoid these errors in the future?

Post edited by kshortt on

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