Question: Mark Duplicate Reads Error- "Value was put into PairInfoMap more than once"
gravatar for JP
3.2 years ago by
United States
JP20 wrote:

Hi everyone,

I am relatively new to galaxy and have been trying to set up a workflow for variant calling used paired end Illumina data (MiSeq).  I aligned the reads using BWA-MEM, but have hit a wall using the Mark Duplicate Reads tool.  I’ve repeatedly received the error “Value was put into PairInfoMap more than once”, and I don’t seem to be able to correct the problem.

I did use the –M option (Mark Shorter Split Hits as Secondary).  Here are the steps I took:

1) FASTQ Groomer on both Fastq Files

2) BWA-MEM with groomed FASTQ’s (-M)

3) Addorreplacereadgroups

4) Clean Sam (on .BAM file)

4) Paired read mate fixer

5) MarkDuplicate Reads (Failed)

I ran the analysis on the public galaxy server.  Any advice/suggestions would be greatly appreciated.



bwa-mem gatk • 1.2k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by JP20
gravatar for Jennifer Hillman Jackson
3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


If you would like to submit this as a bug report, we can examine the data in detail and provide feedback. Send on in from any of the red error datasets using the green bug icon. Please put a link to this biostars post in the comments so we can link the two.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

The report is submitted, thank you for the help!


ADD REPLYlink written 3.2 years ago by JP20

Hi JP, I do not see anything obviously wrong. But I did find a similar post from about 7 months ago. This was someone else, correct?

The MAPQ error has been moved to a warning since that post was written. Perhaps this other fatal error needs to be migrated to be a warning as well. At this point I am opening a ticket for our team to review together. It can be followed here:

Thanks for reporting the problem and hopefully we can resolve it quickly. It is entirely possibly that I missed an input requirement, but we want to rule out a bug/usage issue if there is one. Jen, Galaxy team

ADD REPLYlink written 3.2 years ago by Jennifer Hillman Jackson25k

Hi Jen, 

You are correct, that was another user.....I came across that post as well.  Thank you very much for starting a ticket, I'm very interested to see the result of your review!



ADD REPLYlink written 3.2 years ago by JP20
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