Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

GenomicsDBImport Strange log

SkyWarriorSkyWarrior TurkeyMember ✭✭✭
11:00:36.020 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/exome/scripts/gatk-package-!/com/intel/gkl/native/libgkl_compression.so
11:00:36.675 INFO  GenomicsDBImport - ------------------------------------------------------------
11:00:36.676 INFO  GenomicsDBImport - The Genome Analysis Toolkit (GATK) v4.0.6.0
11:00:36.676 INFO  GenomicsDBImport - For support and documentation go to https://software.broadinstitute.org/gatk/
11:00:36.676 INFO  GenomicsDBImport - Executing as [email protected] on Linux v4.14.53-1-MANJARO amd64
11:00:36.676 INFO  GenomicsDBImport - Java runtime: OpenJDK 64-Bit Server VM v1.8.0_172-b11
11:00:36.676 INFO  GenomicsDBImport - Start Date/Time: July 12, 2018 11:00:36 AM EET
11:00:36.677 INFO  GenomicsDBImport - ------------------------------------------------------------
11:00:36.677 INFO  GenomicsDBImport - ------------------------------------------------------------
11:00:36.677 INFO  GenomicsDBImport - HTSJDK Version: 2.16.0
11:00:36.677 INFO  GenomicsDBImport - Picard Version: 2.18.7
11:00:36.677 INFO  GenomicsDBImport - HTSJDK Defaults.COMPRESSION_LEVEL : 2
11:00:36.677 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
11:00:36.678 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
11:00:36.678 INFO  GenomicsDBImport - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
11:00:36.678 INFO  GenomicsDBImport - Deflater: IntelDeflater
11:00:36.678 INFO  GenomicsDBImport - Inflater: IntelInflater
11:00:36.678 INFO  GenomicsDBImport - GCS max retries/reopens: 20
11:00:36.678 INFO  GenomicsDBImport - Using google-cloud-java patch 6d11bef1c81f885c26b2b56c8616b7a705171e4f from https://github.com/droazen/google-cloud-java/tree/dr_all_nio_fixes
11:00:36.678 INFO  GenomicsDBImport - Initializing engine
11:00:37.070 INFO  IntervalArgumentCollection - Processing 249250621 bp from intervals
11:00:37.088 INFO  GenomicsDBImport - Done initializing engine
Created workspace /mnt/D/ExomeAnalysis/All_GVCFS/process/Part1/chr1
11:00:37.326 INFO  GenomicsDBImport - Vid Map JSON file will be written to chr1/vidmap.json
11:00:37.326 INFO  GenomicsDBImport - Callset Map JSON file will be written to chr1/callset.json
11:00:37.326 INFO  GenomicsDBImport - Complete VCF Header will be written to chr1/vcfheader.vcf
11:00:37.326 INFO  GenomicsDBImport - Importing to array - chr1/genomicsdb_array
11:00:37.327 INFO  ProgressMeter - Starting traversal
11:00:37.328 INFO  ProgressMeter -        Current Locus  Elapsed Minutes     Batches Processed   Batches/Minute
11:00:37.432 INFO  GenomicsDBImport - Starting batch input file preload
11:00:41.444 INFO  GenomicsDBImport - Finished batch preload
11:00:41.444 INFO  GenomicsDBImport - Importing batch 1 with 50 samples
Buffer resized from 16969bytes to 32739
Buffer resized from 16987bytes to 32763
Buffer resized from 16963bytes to 32732
Buffer resized from 16979bytes to 32757
Buffer resized from 16981bytes to 32708
Buffer resized from 16985bytes to 32544
Buffer resized from 16989bytes to 32747
Buffer resized from 16967bytes to 32710
Buffer resized from 16967bytes to 32696
Buffer resized from 16981bytes to 32703
Buffer resized from 16985bytes to 32742
Buffer resized from 16989bytes to 32714
Buffer resized from 16989bytes to 32747
Buffer resized from 16973bytes to 32707

This is something that I did not see before. GATK is used for the task. I am using single interval per import so I am not using the new features for the moment. (My perl script is still faster than anything I tried locally. B) )

Issue · Github
by Sheila

Issue Number
Last Updated


Sign In or Register to comment.