How to reduce the processing time of BwaMemIndexImageCreator

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Ganesh P Kumar

• June 25, 2020 07:10

Hi, 
I am trying to create an Image Index file for PathSeq Pipeline. I am using the Microbiome reference fasta file of 250 GB is taking around 14 days to complete in server  Is there a way to reduce the time taken to complete the process?

System configuration

Processor: 2.30 GHz x64 core 

RAM: 512 GB 

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  Bhanu Gandham

  • June 28, 2020 00:39

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

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  danilovkiri

  • June 29, 2020 11:26

  Hi Ganesh P Kumar

  I guess there is nothing to be done here given your reference genome size. BwaMemIndexImageCreator does basically the same as `bwa index -a bwtsw` which takes a couple of hours for GRCh38 (3GB). Parallelization options are available neither for bwa nor for BwaMemIndexImageCreator. 

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