GATK mark duplicates error

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Kshama Aswath

• July 22, 2020 20:26
• Edited

I was running mark duplicates and I get this following error. Nothing ran. I see that older versions of GATK had this issue and I thought it was fixed. This is the version and other info. on my command executed etc. 

Not sure if this is gatk issue or my machine!

Any help would be greatly appreciated!

a) GATK version used

GATK/4.1.8.0

b) Exact GATK commands used

gatk MarkDuplicates -I ../sample_S10.bam -O sample_S10_dedup.bam -M sample_S10_dedup_metrics.txt

c) The entire error log if applicable.

INFO: Failed to detect whether we are running on Google Compute Engine.

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  Kshama Aswath

  • July 22, 2020 21:11

  So adding to the above post:

  even if it is a "harmless" error and I can ignore it,  could it be a memory issue? I ran it default and did not specify any memory allotment. If that is the case, is there a guide on memory needed ( roughly) on different tools. I understand input file sizes varies and it is hard to say exactly how much to allot, but a ball park idea could hlep. Thankyou !

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  Genevieve Brandt (she/her)

  • July 23, 2020 13:18

  Hi Kshama Aswath, please post the entire error message so we can look into the problem. 

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