Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

GenomicsDBImport function is not executing: Aborted (core dumped)

Follow
Avatar
Tanay Biswas

I am trying to call somatic SNVs using the following pipeline: https://gatk.broadinstitute.org/hc/en-us/articles/360035531132--How-to-Call-somatic-mutations-using-GATK4-Mutect2#article-comments

I am getting errors while making GenomicsDBImport. I have read the following link: https://gatk.broadinstitute.org/hc/en-us/articles/360036459392-GenomicsDBImport

Still, I'm not able to create a GenomicsDB. An output folder is generating but in the next step while creating PON, is is not generating the output.

 

 

REQUIRED for all errors and issues:
a) GATK version used: gatk-4.2.5.0
b) Exact command used: java -Xmx50g -jar /home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport -R /home/tbiswas/hg19.fa --genomicsdb-workspace-path /scratch/tbiswas/pon_db2 --batch-size 1 -L /home/tbiswas/SureSelectV6_S07604514_hs_hg19/Covered.bed -V /home/tbiswas/gatk_output/IITK-P4-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P5-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P6-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P8-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P12-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P13-BD.vcf.gz -V /home/tbiswas/gatk_output/IITK-P14-BD.vcf.gz
c) Entire program log:

[tbiswas@hpc450 ~]$ java -Xmx50g -jar /home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar GenomicsDBImport -R /home/tbiswas/hg19.fa --genomicsdb-workspace-path /scratch/tbiswas/pon_db2 --batch-size 1 -L /home/tbiswas/SureSelectV6_S07604514_hs_hg19/Covered.bed -V /home/tbiswas/gatk_output/P4-BD.vcf.gz -V /home/tbiswas/gatk_output/P5-BD.vcf.gz -V /home/tbiswas/gatk_output/P6-BD.vcf.gz -V /home/tbiswas/gatk_output/P8-BD.vcf.gz -V /home/tbiswas/gatk_output/P12-BD.vcf.gz -V /home/tbiswas/gatk_output/P13-BD.vcf.gz -V /home/tbiswas/gatk_output/P14-BD.vcf.gz


16:04:34.082 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/tbiswas/softwares/gatk-4.2.5.0/gatk-package-4.2.5.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
Aug 22, 2022 4:04:34 PM shaded.cloud_nio.com.google.auth.oauth2.ComputeEngineCredentials runningOnComputeEngine
INFO: Failed to detect whether we are running on Google Compute Engine.
16:04:34.824 INFO  GenomicsDBImport - ------------------------------------------------------------
16:04:34.824 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.2.5.0
16:04:34.825 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
16:04:34.825 INFO  GenomicsDBImport - Executing as tbiswas@hpc450 on Linux v3.10.0-327.el7.x86_64 amd64
16:04:34.825 INFO  GenomicsDBImport - Java runtime: Java HotSpot(TM) 64-Bit Server VM v1.8.0_221-b11
16:04:34.825 INFO  GenomicsDBImport - Start Date/Time: 22 August, 2022 4:04:33 PM IST
16:04:34.825 INFO  GenomicsDBImport - ------------------------------------------------------------
16:04:34.825 INFO  GenomicsDBImport - ------------------------------------------------------------
16:04:34.826 INFO  GenomicsDBImport - HTSJDK Version: 2.24.1
16:04:34.826 INFO  GenomicsDBImport - Picard Version: 2.25.4
16:04:34.826 INFO  GenomicsDBImport - Built for Spark Version: 2.4.5
16:04:34.826 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
16:04:34.826 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
16:04:34.826 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
16:04:34.826 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
16:04:34.826 INFO  GenomicsDBImport - Deflater: IntelDeflater
16:04:34.826 INFO  GenomicsDBImport - Inflater: IntelInflater
16:04:34.826 INFO  GenomicsDBImport - GCS max retries/reopens: 20
16:04:34.827 INFO  GenomicsDBImport - Requester pays: disabled
16:04:34.827 INFO  GenomicsDBImport - Initializing engine
16:04:36.217 INFO  FeatureManager - Using codec BEDCodec to read file file:///home/tbiswas/SureSelectV6_S07604514_hs_hg19/Covered.bed
16:04:38.511 INFO  IntervalArgumentCollection - Processing 60456963 bp from intervals
16:04:38.564 WARN  GenomicsDBImport - A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer. If GVCF data only exists within those intervals, performance can be improved by aggregating intervals with the merge-input-intervals argument.
16:04:38.641 INFO  GenomicsDBImport - Done initializing engine
16:04:38.982 INFO  GenomicsDBLibLoader - GenomicsDB native library version : 1.4.3-6069e4a
16:04:38.984 INFO  GenomicsDBImport - Vid Map JSON file will be written to /scratch/tbiswas/pon_db2/vidmap.json
16:04:38.984 INFO  GenomicsDBImport - Callset Map JSON file will be written to /scratch/tbiswas/pon_db2/callset.json
16:04:38.984 INFO  GenomicsDBImport - Complete VCF Header will be written to /scratch/tbiswas/pon_db2/vcfheader.vcf
16:04:38.984 INFO  GenomicsDBImport - Importing to workspace - /scratch/tbiswas/pon_db2
16:25:03.019 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:06.097 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:08.708 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:11.586 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:14.377 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:16.896 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:19.653 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:22.306 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:24.991 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:27.558 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:30.025 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:32.486 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:35.016 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:37.474 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:39.962 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:42.390 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:45.145 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:47.676 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:50.250 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:52.786 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:55.335 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:25:57.792 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:00.236 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:02.767 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:05.304 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:07.963 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:10.404 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:12.947 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:15.389 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:17.815 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:20.467 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:22.898 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:25.435 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:27.922 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:30.348 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:32.777 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:35.324 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:37.753 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:40.185 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:42.652 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:45.071 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:47.497 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:50.075 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:52.506 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:54.932 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:57.355 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:26:59.785 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:02.221 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:04.654 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:07.308 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:09.737 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:12.166 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:15.129 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:18.050 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:20.576 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:23.010 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:25.478 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:27.952 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:30.379 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:32.809 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:35.523 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:38.061 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:40.488 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:42.918 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:45.400 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:47.931 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:50.449 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:52.868 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:55.299 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:27:57.769 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:00.189 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:02.613 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:05.138 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:07.690 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:10.220 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:12.747 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:15.182 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:17.627 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:20.051 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:22.479 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:25.106 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:27.537 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:29.968 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:32.414 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:34.984 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:37.508 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:40.032 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:42.458 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:44.883 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:47.579 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:50.176 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:52.705 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:55.312 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:28:57.928 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:29:00.364 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:29:02.800 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:29:05.229 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:29:07.674 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
16:29:10.277 INFO  GenomicsDBImport - Importing batch 1 with 1 samples
terminate called after throwing an instance of 'GenomicsDBConfigException'
  what():  GenomicsDBConfigException : Syntax error in JSON file /tmp/loader_8730616673636696850.json
Aborted (core dumped)
[tbiswas@hpc450 ~]$ 

Thank you.

 

Regards,

Tanay

 

0

2 comments

Sort by Date Votes
  • Avatar
    Anthony DiCi

    Hi Tanay Biswas,

    Thank you for writing to the GATK forum. I hope that we can help you sort this out.

    After reviewing your ticket, I noticed the following issues. 

    1. You are using an outdated version of GATK. The current version is 4.2.6.1; you used an older version, 4.2.5.0.
    2. The GenomicsDBImport tool index that you linked is for an even older version of GATK than 4.2.5.0; it is from GATK version 4.0.5.2.
    3. You are not running with the correct GATK wrapper script.
    4. You are using a Panel of Normals (PON) with less than 50 samples.

    Given those issues, I strongly recommend first compiling a panel of normals with at least 50 samples. When you have those, please rerun the pipeline with the proper GATK wrapper script while using the latest version of GATK and GenomicsDBImport (4.2.6.1). Please find some additional resources below.

    Panel of Normals

    GATK4 Command-Line Syntax

    GenomicsDBImport 4.2.6.1

    I hope this helps! Please let me know if this solves your problem.

    Best,

    Anthony

    0
    Comment actions Permalink
  • Avatar
    Anthony DiCi

    Hi Tanay Biswas,

    We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll make you a follow-up ticket to pick up where we left off.

    Thank you again for your contribution to the GATK forum!

    Best,
    Anthony

    0
    Comment actions Permalink

Please sign in to leave a comment.

Welcome

Forum Guidelines

GATK Announcements

Become a GATK Guru

Read Before You Post

Get Email Notifications

GATK Team Out of Office

The GATK team will be out of office during December 9th 2022 to January 9th 2022 in observance of the holidays. We will not be able to answer posts from within this period. If you are still experiencing issues when we are back, please re-post your inquiry.

Didn't find what you were looking for?

New post

Quick Links

GATK Latest Releases

Known Issues & Troubleshooting

Submitting a Bug Report

How to Track a Github issue

GATK on the Cloud with Terra

Recent GATK News

GATK Blog Posts

GATK Twitter Page

About the GATK community

  • 133,119 Total Users
  • 0 Comments
  • 0 Posts
  • 0 Votes
Powered by Zendesk