GATK 4.3 configuration
1
0
Entering edit mode
21 months ago
wonde2000 • 0

Dear all,

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

enter image description here

cofig GATK • 1.1k views
ADD COMMENT
0
Entering edit mode

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 wondossen@planetsmasher.hgen.slu.se 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)
ADD REPLY
1
Entering edit mode

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-

ADD REPLY
0
Entering edit mode
21 months ago
lacb ▴ 120

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.

ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1679 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6