Funcotator: Unable to open SQLite DB for COSMIC

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AB

• June 03, 2022 19:23
• Edited

a) GATK version used: GATK-4.2.6.1
b) Exact command used: 

gatk-4.2.6.1/gatk Funcotator \
-R Homo_sapiens_assembly19.fasta \
-V 1170_mutect2/1170_filtered.vcf.gz \
-O 1170_mutect2/1170.maf \
--output-file-format MAF \
--data-sources-path 1170_mutect2/pipeline/funcotator_dataSources \
--ref-version hg19

c) Entire program log:

Failed to load native library:sqlite-3.36.0.3-7efeb603-ddef-40cc-b15d-4a95cd1524ad-libsqlitejdbc.so. osinfo: Linux/x86_64

java.lang.UnsatisfiedLinkError: /tmp/sqlite-3.36.0.3-7efeb603-ddef-40cc-b15d-4a95cd1524ad-libsqlitejdbc.so: /tmp/sqlite-3.36.0.3-7efeb603-ddef-40cc-b15d-4a95cd1524ad-libsqlitejdbc.so: failed to map segment from shared object: Operation not permitted

SQLite is installed.

Data source was downloaded using:

gatk FuncotatorDataSourceDownloader --somatic --validate-integrity --extract-after-download

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• 

  Genevieve Brandt (she/her)

  • June 06, 2022 19:58

  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

  • June 07, 2022 20:25

  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)

  • June 13, 2022 21:48

  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

  • June 13, 2022 22:08

  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

  • June 14, 2022 17:29

  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)

  • June 14, 2022 17:37

  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

  • June 14, 2022 17:38

  Thank you!

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