Picard Error with SAM File
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Entering edit mode
6.8 years ago

Hi

I'm new in bioinformatics. I was trying to add Read Group to a SAM file by Picard and I got this error:

{Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing text SAM file. MRNM not specified but flags indicate mate mapped; File /home/masoud/NGS/Samples/54992.sam; Line 744
Line: MISEQ:131:000000000-A565J:1:1101:12427:6217    65    chr13    32904990    219    214M36S    *    0    0    GGGGACTACTACTGTATGTGCATTGAGAGTTTTTATACTAGTGATTTTAAACTATAATTTTTGCAGAATGTGAAAAGCTATTTTTCCAATCATGATGAAGGTCTGAAGAAAAATGATAGATTTATCGCTTCTGTGACAGACAGTGAAAACACAAATCAAAGAGAAGCTGCAAGTCATGGTAAGTCCTCTGTTTAGTTGAACTACAGGTTTTTTTTTGTTGTTGTTTTGCTTTTTTTTTTTTTTGATGTGG    1AAAADCCFFFFGGG3FGGDFAGHBHHGH1FGHGHHHHHGCDDGHGHHGAEGHHHHHHHHHHGGHHFEGHHG22DAAGHHHFHHHHHHGHHHHH2GHHDFFGHHFHHGFHHGHFHHHHHHHHHHHHHGHHGHHHHHHHHHHHHHHF>GHHFGHFGHHHFFHHHGHHHGHHGFHGDDG>GF2FGGGHHHHGHHHGHHF1F1?GHFFGFHDGGGGGGGCHHFHHHCGHHG0;CFHHGGGGG@@@?#######    AS:i:206    XS:i:0    XF:i:0    XE:i:5    NM:i:2}


What is this? What should I do to solve it?

Thank you

Masoud

SAM Picard • 3.9k views
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Entering edit mode

How did you create that SAM file? Whichever aligner you used has a bug. I or someone else here could write a little python program to get around this particular error, but I worry about the validity of the alignments in general if the output is broken like this.

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Entering edit mode

Hi,

Please use appropriate tags when you create posts. You'd used "forum" (which is not relevant here), and I changed it to "sam" and "picard". The system is designed to alert people subscribed to certain tags when new posts are created with those tags, so you stand a better chance of getting faster responses if you use the right tags.

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Entering edit mode
6.8 years ago

This is one of the known discrepancies between the SAMtools specification and Picard's validation of the format: see http://sourceforge.net/p/samtools/mailman/samtools-devel/thread/AB0E0502-911B-444C-B112-AA9248C7AA00@sanger.ac.uk/