The current GATK version is 3.8-0
Examples: Monday, today, last week, Mar 26, 3/26/04

#### Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

You can opt in to receive email notifications, for example when your questions get answered or when there are new announcements, by following the instructions given here.

#### ☞ Got a problem?

1. Search using the upper-right search box, e.g. using the error message.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

#### ☞ Formatting tip!

Wrap blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ` ) each to make a code block as demonstrated here.

GATK version 4.beta.3 (i.e. the third beta release) is out. See the GATK4 beta page for download and details.

# BQSR fails giving Malformed read

Member

Dear GATK Team,

I am running a pipeline on several high coverage human individuals that have been mapped using bwa and processed using samtools, picard and gatk. The bam-files pass ValidateSam from picard, but when I run the bqsr step some of them fails giving a Malformed read error (using -filterMBQ does not help in this case). I tracked down the error to bamfiles that ends with a paired end read where the mate maps in the beginning of the contig (in my case human mtDNA).

Eg, this will make it crash:

readX 177 MT 16558 37 7S2M2I10M80S = 294 -16176 GACCTGTGATCC...
readY 177 MT 16558 37 7S2M2I10M80S = 238 -16232 GACCTGTGATCC...
readZ 113 MT 16558 37 7S2M2I10M80S = 273 -16197 GACCTGTGATCC...
[END]

where a file ending like this wont crash:

readX 83 MT 16469 60 101M = 16246 -324 TGGGGGTAGCTAAAGTGAAC...
readY 147 MT 16469 60 101M = 16267 -303 TGGGGGTAGCTAAAGTGA...
readZ 147 MT 16469 60 101M = 16193 -377 TGGGGGTAGCTAAAGTGAAC...
[END]

I am running GATK v2.3-9-ge5ebf34, but the same error occurs using GATK v-2.2-3 (my previous version). I can genotype the files using UnifiedGenotyper without any problem as well.

This is the error:

##### ERROR stack trace

at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203) at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468) at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source) at java.util.concurrent.FutureTask.run(Unknown Source) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)

##### ERROR ------------------------------------------------------------------------------------------

Cheers,

Simon

Tagged:

• Member

When I look at it, it could just as well be due to the soft-clipping of the reads.

Cheers,

Simon

edited January 2013

Hi Simon,

The tool shouldn't be freaking out over these. Could you please upload a bug report so we can take a closer look?

bug report instructions

• Member

Hi, just out of curiosity, in your analysis did you happen to run local realignment with GATK. I'm asking b/c I am wondering if you need to something to fix the mate pair (the sam flags) in your bam file. I think the local realignment process in GATK does that, otherwise I think you would need to run FixMatePairs from the picard suite. Just a guess.

• Member

Hi Kurt,
Yes, I did local realignment using GATK, and did it for all files - only some were giving me these problems.

Geraldine: I will upload a bug report.

Cheers

• Member

Dear Geraldine,

I was not able to upload my tar-ball to your ftp, it wouldnt let me write there - even using the right upload credentials

Instead I shared the tar-file in my dropbox, I hope it works for you. It contains "MT:16001-16569", for a sample that will give the error and a version where I removed the offending reads (the last ones with the soft-clipping in the cigar) which runs without problems.

https://www.dropbox.com/s/w9erfkifo52q4k4/gatk_bqsr_simon_bug.tar.gz

Best,

Simon

Thanks Simon, we can work with that. We seem to be having some issues with the FTP server today.

I'll let you know what we come up with. Thanks for reporting the bug!

• Member

Great - thank you very much!

Hi Simon,

It looks like you have removed your files so that we cannot access them.

• Member

Cheers,

Simon