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Funcotator: Unable to open SQLite DB for COSMIC

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    Genevieve Brandt (she/her)

    Hi AB,

    Thanks for writing in with this issue so that we can get GATK working for you! Can you give more information about your operating system and the version of SQLite you have installed? Can you also share your libc version as well?

    Thank you,

    Genevieve

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    AB

    Hi Genevieve-Brandt-she-her,

    I am using a remote server which is running RedHat 7.7

    SQLite version: 3.32.3 (Installed using conda)

    libc version: 2.17

    Thank you.

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    Genevieve Brandt (she/her)

    Hi AB,

    Thank you for the follow up information. One easy solution would be to run GATK through our docker image, if that is possible on your server.

    This could potentially be a permissions issue with the temp folder where GATK has stored SQLite. Could you look at the permissions for /tmp and the .so file (/tmp/sqlite-3.36.0.3-7efeb603-ddef-40cc-b15d-4a95cd1524ad-libsqlitejdbc.so)? With ls -l

    Let us know what you find. 

    Best,

    Genevieve

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    AB

    Hi Genevieve-Brandt-she-her,

    I am working on broad institute server, so I have not installed gatk(as root). I have been using it just by extracting the latest release and running the executable. I have read, write access to the /tmp/ folder but there is no .so file present.

    I am assuming this is the case as I have not 'installed' GATK completely. I tried doing that but I could not do it as I do not have root access.

     

    Thank you.

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    AB

    Hi Genevieve-Brandt-she-her,

    After you pointed out about the TEMP folder which GATK uses for SQLite, I ran Funcotator using --tmp-dir flag and got it running. Thank you!

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    Genevieve Brandt (she/her)

    AB great news! If there are other issues you come across indicating you might not have GATK installed properly, take a look at this quick start guide: https://github.com/broadinstitute/gatk#quick-start-guide

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    AB

    Thank you!

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