Question: Picard Error with SAM File
gravatar for edizadeh.masoud
4.3 years ago by
edizadeh.masoud0 wrote:


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

what is this ? what should i do to solve it ?

Thank you 



sam picard • 2.7k views
ADD COMMENTlink modified 3.4 years ago by Biostar ♦♦ 20 • written 4.3 years ago by edizadeh.masoud0

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.

ADD REPLYlink written 4.3 years ago by Devon Ryan94k


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.

ADD REPLYlink written 4.3 years ago by RamRS26k
gravatar for harold.smith.tarheel
4.3 years ago by
United States
harold.smith.tarheel4.5k wrote:

This is one of the known discrepancies between the SAMtools specification and Picard's validation of the format: see

ADD COMMENTlink modified 3 months ago by RamRS26k • written 4.3 years ago by harold.smith.tarheel4.5k
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