Hi,
I tried to use GenotypeGVCFs from GATK4.beta.1, but there seems to be still a bug with the --variants statement. At first I gave a list of my g.VCF files to it (ending .list as it worked in GATK3.7), but got an error message that no suitable codecs have been found. Giving multiple statements containing always one of my input files produced the error that I am only allowed to set this option once, but running GenotypeGVCFs with only one input g.VCF worked (no longer as I tried to use just this sample within the input list). Was there a change since 3.7 or is this a bug?
In addition, I'm woundering how to get the full stack trace, as -DGATK_STACKTRACE_ON_USER_EXCEPTION was somehow recogniced as -D (A USER ERROR has occurred: Argument '[D, dbsnp]' cannot be specified more than once.) and -GATK_STACKTRACE_ON_USER_EXCEPTION just produced no change in the log.
Thanks in advance
Johannes
Using GATK jar /home/uni08/geibel/software/gatk-4.beta.1/gatk-package-4.beta.1-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=1 -Dsnappy.disable=true -Xmx220g -jar /home/uni08/geibel/software/gatk-4.beta.1/gatk-package-4.beta.1-local.jar GenotypeGVCFs -R /home/uni08/geibel/chicken/chickenrefgen/galGal5_Dec2015/galGal5.fa --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/VCF_test/input_chr26.list --useNewAFCalculator -L /home/uni08/geibel/chicken/chickenrefgen/galGal5_Dec2015/contigs_chr26.intervals --dbsnp /home/uni08/geibel/chicken/chickenrefgen/ENSEMBL_20170106/Gallus_gallus.updated.vcf -O /usr/users/geibel/chicken/pool_sequence_nov2016/data/VCF_test/IndandPool_chr26.raw.vcf
[July 7, 2017 2:35:20 PM CEST] GenotypeGVCFs --output /usr/users/geibel/chicken/pool_sequence_nov2016/data/VCF_test/IndandPool_chr26.raw.vcf --useNewAFCalculator true --dbsnp /home/uni08/geibel/chicken/chickenrefgen/ENSEMBL_20170106/Gallus_gallus.updated.vcf --variant /usr/users/geibel/chicken/pool_sequence_nov2016/data/VCF_test/input_chr26.list --intervals /home/uni08/geibel/chicken/chickenrefgen/galGal5_Dec2015/contigs_chr26.intervals --reference /home/uni08/geibel/chicken/chickenrefgen/galGal5_Dec2015/galGal5.fa --annotateNDA false --heterozygosity 0.001 --indel_heterozygosity 1.25E-4 --heterozygosity_stdev 0.01 --standard_min_confidence_threshold_for_calling 10.0 --max_alternate_alleles 6 --max_genotype_count 1024 --sample_ploidy 2 --group StandardAnnotation --onlyOutputCallsStartingInIntervals false --interval_set_rule UNION --interval_padding 0 --interval_exclusion_padding 0 --readValidationStringency SILENT --secondsBetweenProgressUpdates 10.0 --disableSequenceDictionaryValidation false --createOutputBamIndex true --createOutputBamMD5 false --createOutputVariantIndex true --createOutputVariantMD5 false --lenient false --addOutputSAMProgramRecord true --addOutputVCFCommandLine true --cloudPrefetchBuffer 40 --cloudIndexPrefetchBuffer -1 --disableBamIndexCaching false --help false --version false --showHidden false --verbosity INFO --QUIET false --use_jdk_deflater false --use_jdk_inflater false --disableToolDefaultReadFilters false
[July 7, 2017 2:35:20 PM CEST] Executing as geibel@gwdu101 on Linux 3.10.0-327.36.3.el7.x86_64 amd64; OpenJDK 64-Bit Server VM 1.8.0_111-b15; Version: 4.beta.1
[July 7, 2017 2:35:33 PM CEST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 0.22 minutes.
Runtime.totalMemory()=985661440
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A USER ERROR has occurred: Cannot read /usr/users/geibel/chicken/pool_sequence_nov2016/data/VCF_test/input_chr26.list because no suitable codecs found
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Use -DGATK_STACKTRACE_ON_USER_EXCEPTIONto print the stack trace.