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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

GATK HaplotypeCaller OS Error - non-existent file or directory

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    Genevieve Brandt (she/her)

    Hi Daniela Zarate,

    Hmm, this is a strange error. My first advice would be to use a newer version of GATK. We are now on 4.2 and so 4.0.1.1 is quite outdated. There have been a lot of great updates since then that might help this issue! 

    My other thought is that this could be from GATK not installed correctly, have you run other GATK commands successfully with this same installation?

    Best,

    Genevieve

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    Daniela Zarate

    Hi Genevieve, 

    Thanks for the reply! Yes, it is a strange issue. I believe there are a few things that it might be, although I haven't narrowed it down. {1} it could be an issue that the names of the directories and files are too long. There's some information that suggests that absolute paths with >96 characters can throw this OS error message. {2} this could be an issue with the HPC environment I am using and the nodes which are deployed. I notice that this script will run successfully on certain nodes and not on others. Perhaps there is some underlying node configuration that is causing the issue. I am working with my HPC staff to resolve this but so far there's no clear answer. 

    The GATK 4.0.11 is quite outdated and the only reason I'm using it is because it is the default on the HPC I use. As this is a shared resource and many people use it, I'm sure the installation was done correctly....? I have run other jobs with this GATK successfully. Although I think I will import my own updated GATK for use on the HPC from now on.....thanks again. 

     

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    Genevieve Brandt (she/her)

    Thanks for posting the helpful information Daniela, I'm sure this will be very useful for other GATK users in the future!

    Please let us know if your HPC staff is not able to figure out a resolution and I will ask around in my team if there is anything else you can try.

    Genevieve

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