Base recalibration -Java run time error and no sequence dictionary

Question

[priya.bmg]

Hello

I am stuck with base recalibration step in NGS analysis. Used this command for the base calibration step: gatk BaseRecalibrator -I sample1.bam -R gch38.fa --known-sites GCF_000001405.39 -O recal_data.table I got the following warning:

WARN IndexUtils - Feature file "file :////scicore/home/cichon/GROUP/bwa-mem2/GCF_000001405.39" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary
12:16:28.590 INFO  BaseRecalibrator - Shutting down engine
[August 16, 2021 12:16:28 PM CEST] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.88 minutes.
Runtime.totalMemory()=2594897920
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space

I used the following command to update sequence dictionary using the command below but still got the above error:

gatk UpdateVCFSequenceDictionary -V GCF_000001405.39.gz --source-dictionary gch38dict --output resource_newcontiglines.vcf.gz 

There is problem in running the base recalibration step because there is no dcitionary of the vcf file as well as java run time memory error?. Have someone come across this issue?

Thanks

Answer 1

[brunobsouzaa]

For BaseRecalibrator, use the -D argument and give the path to your .dict file

For java, use the -Xmx argument before calling GATK