GATK 4.3 configuration

Question

[wonde2000]

Dear all,

I am trying to run gatk 4.3. However I got the following message. I would appreciate for your technical comment/help.

[Pierre Lindenbaum]

please, don't put a screenshot when you can copy-n-paste the text

[wonde2000]

Dear All, Thank you for your suggestions. This is my first time to run GATK and got the following error.

(base) module load gatk
(/opt/sw/gatk/4.3/gatk4_env) gatk BaseRecalibrator -I ../data/Afar_rD/Afar_1_dedup.bam -R ../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --known-sites ../GATK_reso/
ARS1.2PlusY_BQSR.vcf.gz -O Afar1_data.table
Using GATK jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar
Running:
    java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar BaseRecalibrator -I ../data/Afar_rD/Afar_1_dedup.bam -R ../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa --known-sites ../GATK_reso/ARS1.2PlusY_BQSR.vcf.gz -O Afar1_data.table
12:43:10.137 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/export/opt/sw/gatk/4.3/gatk4_env/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
12:43:10.619 INFO  BaseRecalibrator - ------------------------------------------------------------
12:43:10.619 INFO  BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.3.0.0
12:43:10.619 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
12:43:10.620 INFO  BaseRecalibrator - Executing as [e-mail] on Linux v3.10.0-693.21.1.el7.x86_64 amd64
12:43:10.620 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v11.0.13+7-b1751.21
12:43:10.621 INFO  BaseRecalibrator - Start Date/Time: February 13, 2023 at 12:43:10 PM CET
12:43:10.621 INFO  BaseRecalibrator - ------------------------------------------------------------
12:43:10.621 INFO  BaseRecalibrator - ------------------------------------------------------------
12:43:10.622 INFO  BaseRecalibrator - HTSJDK Version: 3.0.1
12:43:10.622 INFO  BaseRecalibrator - Picard Version: 2.27.5
12:43:10.622 INFO  BaseRecalibrator - Built for Spark Version: 2.4.5
12:43:10.622 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
12:43:10.622 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
12:43:10.623 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
12:43:10.623 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
12:43:10.623 INFO  BaseRecalibrator - Deflater: IntelDeflater
12:43:10.623 INFO  BaseRecalibrator - Inflater: IntelInflater
12:43:10.623 INFO  BaseRecalibrator - GCS max retries/reopens: 20
12:43:10.623 INFO  BaseRecalibrator - Requester pays: disabled
12:43:10.624 INFO  BaseRecalibrator - Initializing engine
12:43:10.627 INFO  BaseRecalibrator - Shutting down engine
[February 13, 2023 at 12:43:10 PM CET] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=2109734912
***********************************************************************

A USER ERROR has occurred: Fasta dict file file:///export/proj/ethiopian_cattle/NOBACKUP/../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.dict for reference file:///export/proj/ethiopian_cattle/NOBACKUP/../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
(/opt/sw/gatk/4.3/gatk4_env)

[GenoMax]

A USER ERROR has occurred: Fasta dict file file:///export/proj/ethiopian_cattle/NOBACKUP/../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.dict for reference file:///export/proj/ethiopian_cattle/NOBACKUP/../reference/Bos_taurus.ARS-UCD1.2.dna.toplevel.fa does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.

You need to create a dictionary for your fasta file. Instructions for doing that are at: https://gatk.broadinstitute.org/hc/en-us/articles/360036729911-CreateSequenceDictionary-Picard-

Answer 1

[lacb]

To use GATK tools you have to use the command gatk followed by the tool name you want to use: gatk <ToolName>

For example to use the BuildBamIndex you have to type BuildBamIndex -I input.bam (and add other argument if you need it).

A list of GATK 4.3 tools and their documentation is available here and for other versions its here.

[wonde2000]

Thank you so much! your suggestion works for GATK conf. problem. The problem was I did not prepared ".dict" and ".fai" files.