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GATK4 beta2 GenotypeGVCFs produces VCF with no records, just a header
GATK4 beta2 GenotypeGVCFs produces a VCF with no records on my test data. The file does contain a valid VCF header.
The commands that I used for GenomicsDBImport and GenotypeGVCFs are below. Both were run on the GATK4 beta2 jar.
gatk-launch --javaOptions '-Xms500m -Xmx28665m -XX:+UseSerialGC -Djava.io.tmpdir=/data/run/tmpKVSMhn' GenomicsDBImport -V DA_123_01.vcf.gz -V DA_123_02.vcf.gz -V DA_123_03.vcf.gz -V DA_123_04.vcf.gz -V DA_123_05.vcf.gz -V DA_123_06.vcf.gz -V DA_123_07.vcf.gz -V DA_123_08.vcf.gz --genomicsDBWorkspace DEV_1066_Chr_01 --intervals Chr_01 gatk-launch --javaOptions '-Xms500m -Xmx28665m -XX:+UseSerialGC -Djava.io.tmpdir=/data/run/tmpKVSMhn' GenotypeGVCFs -R ./my_species.fa -V gendb://DEV_1066_Chr_01 -G StandardAnnotation -newQual -O DEV_1066_Chr_01.vcf.gz
The output of both tools does not show anything strang. The GenotypeGVCFs tool finishes with these statements:
17:07:24.554 INFO ProgressMeter - Chr_01:38007262 12.4 17243000 1394831.5 17:07:34.561 INFO ProgressMeter - Chr_01:38743870 12.5 17590000 1403959.7 GENOMICSDB_TIMER,GenomicsDB iterator next() timer,Wall-clock time(s),500.6120602850972,Cpu time(s),450.9598250043053 17:07:37.965 INFO ProgressMeter - Chr_01:39060683 12.6 17742934 1409782.4 17:07:37.965 INFO ProgressMeter - Traversal complete. Processed 17742934 total variants in 12.6 minutes. 17:07:37.975 WARN IntelDeflaterFactory - IntelDeflater is not supported, using Java.util.zip.Deflater 17:07:37.976 INFO GenotypeGVCFs - Shutting down engine [July 20, 2017 5:07:37 PM CEST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 12.61 minutes. Runtime.totalMemory()=506986496
The gVCF files were produced with GATK4 beta1. Is there a way that this issue can be solved or that I can further debug this issue?