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GenotypeGVCFs - IllegalStateException: VariantContext must contain at least one genotype with likelihoods -- did this VC exceed the max number of alt alleles?
Dear all, I comment on this issue because I have the identical error message but this time in 4.6.2 GATK as found in previous Github tickets for prior versions. Here are the tickets I am referring to : https://github.com/broadinstitute/gatk/issues/7639 https://github.com/broadinstitute/gatk/issues/7933 https://github.com/broadinstitute/gatk/issues/7938
I have used CombineGCVF instead of GenomicsDBImport, but given the discussion here that I found during my debug research, it seems this is not related to it, am I correct ? I only found about GenomicsDB during this debug and while reading the GATK related articles so I will use it afterwards, but unless this is related to this issue, I would prefer to try to debug this first. I don't exclude the possibility that this is an error on my side of course, but this thread led me to have a doubt whether it could be something else ?
I tried with the following : no --genomicsdb-max-alternate-alleles argument, ---genomicsdb-max-alternate-alleles 50 after looking on the documentation, --genomicsdb-max-alternate-alleles 100 as a test, -genomicsdb-max-alternate-alleles 6 which instantaneously refused saying it had to be one more that the genotype, --genomicsdb-max-alternate-alleles 54 based on the error message, all with the same exact error message at the exact same location NC_037639.1:14985690.
Same error goes by using --all-sites and I also tried t-AX ExcessHet -AX InbreedingCoeff as suggested in mentioned ticket https://github.com/broadinstitute/gatk/issues/7938.
I am also aware repetitive sequences may lead to a over-estimation of allele numbers, but I am not sure whether this is something I can act upon at the software level (I am new to bioinformatics, just in case).
Elements of context :
- at this stage, I have obtained the input g.vcf.gz, called "all_samples_small.g.vcf.g" which is a pile up of 6 paired-end files treated with HaplotypeCaller (hence the "small" I use it to pre-test the pipeline as far as possible before getting to variant settings on huge files)
- this is about non-human genomics (bees), my gen_ref has worked so far
- the program is not fully automated yet, hence the hard coded names in the program
Side question : I am a bit confused about the fact that the forum GATK is claimed not to be monitored by GATK members anymore, is Github the right way to go as a user from now on ?
Here is the program section and here is the log below. Thanks if you can help !
- Related program-section (bash script)
#Step 1 : HaplotypeCaller (ploidy 2 is the recommended setting for bee genomics in litterature)
for R1_file in $R1_folder/*; do filename=$(basename "$R1_file" _R1_001.fastq) gatk HaplotypeCaller -I ${filename}_merged_aligned.bam -O ${filename}.g.vcf.gz -R $gen_ref -ERC GVCF -ploidy 2 done
#Step 2 : Combining all samples and genotypes with GATK
gatk --java-options "-Xmx10g" CombineGVCFs -R $gen_ref --variant 1.g.vcf.gz --variant 2.g.vcf.gz --variant 3.g.vcf.gz --variant 4.g.vcf.gz --variant 5.g.vcf.gz --variant 6.g.vcf.gz --O all_samples_small.g.vcf.gz
#Step 3 : joint genotyping
gatk --java-options "-Xmx10g" GenotypeGVCFs -R $gen_ref -V all_samples_small.g.vcf.gz --use-new-qual-calculator --genomicsdb-max-alternate-alleles 50 -O all_samples_small_genotyped.vcf.gz
- Here is the log :
Using GATK jar /.../gatk-4.6.2.0/gatk-package-4.6.2.0-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 -Xmx10g -jar /.../gatk-4.6.2.0/gatk-package-4.6.2.0-local.jar GenotypeGVCFs -R /.../ncbi_dataset/ncbi_dataset/data/GCF_003254395.2/GCF_003254395.2_Amel_HAv3.1_genomic.fna -V all_samples_small.g.vcf.gz --use-new-qual-calculator -O all_samples_small_genotyped.vcf.gz 11:02:45.760 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/.../gatk-4.6.2.0/gatk-package-4.6.2.0-local.jar!/com/intel/gkl/native/libgkl_compression.so 11:02:45.918 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:02:45.921 INFO GenotypeGVCFs - The Genome Analysis Toolkit (GATK) v4.6.2.0 11:02:45.921 INFO GenotypeGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/ 11:02:45.921 INFO GenotypeGVCFs - Executing as ... on Linux v4.19.0-27 amd64 11:02:45.921 INFO GenotypeGVCFs - Java runtime: Java HotSpot(TM) 64-Bit Server VM v17.0.11+7-LTS-207 11:02:45.921 INFO GenotypeGVCFs - Start Date/Time: 26 mai 2025 à 11:02:45 CEST 11:02:45.921 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:02:45.921 INFO GenotypeGVCFs - ------------------------------------------------------------ 11:02:45.922 INFO GenotypeGVCFs - HTSJDK Version: 4.2.0 11:02:45.922 INFO GenotypeGVCFs - Picard Version: 3.4.0 11:02:45.922 INFO GenotypeGVCFs - Built for Spark Version: 3.5.0 11:02:45.925 INFO GenotypeGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2 11:02:45.925 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false 11:02:45.925 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true 11:02:45.925 INFO GenotypeGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false 11:02:45.925 INFO GenotypeGVCFs - Deflater: IntelDeflater 11:02:45.926 INFO GenotypeGVCFs - Inflater: IntelInflater 11:02:45.926 INFO GenotypeGVCFs - GCS max retries/reopens: 20 11:02:45.926 INFO GenotypeGVCFs - Requester pays: disabled 11:02:45.926 INFO GenotypeGVCFs - Initializing engine 11:02:46.064 INFO FeatureManager - Using codec VCFCodec to read file file:///.../all_samples_small.g.vcf.gz 11:02:46.133 INFO GenotypeGVCFs - Done initializing engine 11:02:46.177 INFO ProgressMeter - Starting traversal 11:02:46.177 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute 11:02:46.345 WARN InbreedingCoeff - InbreedingCoeff will not be calculated at position NC_037638.1:6259 and possibly subsequent; at least 10 samples must have called genotypes 11:02:56.182 INFO ProgressMeter - NC_037638.1:1606491 0.2 1048000 6285485.8 11:03:03.016 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000843 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000855 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000856 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000857 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000858 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000859 11:03:03.017 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:3000860 11:03:06.186 INFO ProgressMeter - NC_037638.1:3613663 0.3 2353000 7055824.9 11:03:16.187 INFO ProgressMeter - NC_037638.1:5747485 0.5 3728000 7453515.5 11:03:19.913 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:6503346 11:03:19.914 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:6503347 11:03:19.914 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:6503348 11:03:26.191 INFO ProgressMeter - NC_037638.1:7754996 0.7 5044000 7563352.8 11:03:32.518 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:9050253 11:03:36.198 INFO ProgressMeter - NC_037638.1:9797504 0.8 6358000 7626549.4 11:03:46.202 INFO ProgressMeter - NC_037638.1:11944201 1.0 7759000 7755768.4 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388307 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388308 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388309 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388310 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388311 11:03:53.460 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388312 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388313 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388314 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388315 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388316 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388317 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388318 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388319 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388320 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388321 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388322 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388323 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388324 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388325 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388326 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388327 11:03:53.461 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388328 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388329 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388330 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388331 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388332 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388333 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388334 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388335 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388336 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388337 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388338 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388339 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388340 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388341 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388342 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388343 11:03:53.462 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388344 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388345 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388346 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388347 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388348 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388349 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388350 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388351 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388352 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388353 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388354 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388355 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388356 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388357 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388358 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388359 11:03:53.463 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388360 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388361 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388362 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388363 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388364 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388365 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388366 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388367 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388368 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388369 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388370 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388371 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388372 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388373 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388374 11:03:53.464 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388375 11:03:53.465 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388376 11:03:53.465 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:13388377 11:03:56.205 INFO ProgressMeter - NC_037638.1:14033248 1.2 9077000 7777174.8 11:04:06.210 INFO ProgressMeter - NC_037638.1:16060765 1.3 10415000 7808029.2 11:04:16.210 INFO ProgressMeter - NC_037638.1:18113835 1.5 11738000 7822465.1 11:04:26.212 INFO ProgressMeter - NC_037638.1:20366496 1.7 13155000 7890238.4 11:04:33.395 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:21897622 11:04:33.396 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:21897623 11:04:36.213 INFO ProgressMeter - NC_037638.1:22483222 1.8 14557000 7937584.1 11:04:43.028 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:23848367 11:04:43.029 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:23848369 11:04:44.675 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037638.1:24163003 11:04:46.219 INFO ProgressMeter - NC_037638.1:24467772 2.0 15883000 7938721.4 11:04:56.219 INFO ProgressMeter - NC_037638.1:26370270 2.2 17135000 7905907.3 11:05:06.223 INFO ProgressMeter - NC_037639.1:628152 2.3 18451000 7904974.1 11:05:15.608 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:2790561 11:05:15.608 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:2790562 11:05:15.608 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:2790563 11:05:15.608 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:2790564 11:05:15.608 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:2790565 11:05:16.225 INFO ProgressMeter - NC_037639.1:2932841 2.5 19884000 7951108.7 11:05:26.228 INFO ProgressMeter - NC_037639.1:5034351 2.7 21244000 7963961.5 11:05:32.113 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265583 11:05:32.113 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265584 11:05:32.113 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265585 11:05:32.113 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265586 11:05:32.113 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265587 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265588 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265589 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265590 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265591 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265592 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265593 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265594 11:05:32.114 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:6265595 11:05:36.232 INFO ProgressMeter - NC_037639.1:7122897 2.8 22635000 7986239.7 11:05:36.963 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:7255017 11:05:36.964 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:7255018 11:05:36.964 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:7255019 11:05:36.964 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:7255020 11:05:41.132 WARN MinimalGenotypingEngine - Some genotypes contained insufficient data to recalculate site and allele qualities. Site will be skipped at location NC_037639.1:8103070 11:05:46.233 INFO ProgressMeter - NC_037639.1:9122635 3.0 24013000 8001843.9 11:05:56.235 INFO ProgressMeter - NC_037639.1:11159336 3.2 25373000 8010081.1 11:06:06.238 INFO ProgressMeter - NC_037639.1:13131538 3.3 26729000 8016255.0 11:06:15.612 INFO GenotypeGVCFs - Shutting down engine [26 mai 2025 à 11:06:15 CEST] org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs done. Elapsed time: 3.50 minutes. Runtime.totalMemory()=1090519040 org.broadinstitute.hellbender.exceptions.GATKException: Exception thrown at NC_037639.1:14985690 [VC Unknown @ NC_037639.1:14985690 Q. of type=MIXED alleles=[A*, <NON_REF>, AAG, AAGAG, AAGAGAG, AAGAGAGAG, AAGAGAGAGAG, AAGAGAGAGAGAG, AAGAGAGAGAGAGAG] attr={DP=53, ExcessHet=0.00, RAW_MQandDP=[182809, 51]} GT=[[MySample ./. GQ 0 DP 0 PL 0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 {MIN_DP=0}]] filters= at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:144) at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183) at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197) at java.base/java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:179) at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:197) at java.base/java.util.Iterator.forEachRemaining(Iterator.java:133) at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1845) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:509) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:499) at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150) at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.forEachOrdered(ReferencePipeline.java:601) at org.broadinstitute.hellbender.engine.VariantLocusWalker.traverse(VariantLocusWalker.java:132) at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1119) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:150) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:203) at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:222) at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166) at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209) at org.broadinstitute.hellbender.Main.main(Main.java:306) Caused by: java.lang.IllegalStateException: VariantContext at NC_037639.1:14985690must contain at least one genotype with likelihoods -- did this VC exceed the max number of alt alleles? at org.broadinstitute.hellbender.utils.Utils.validate(Utils.java:814) at org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc.AlleleFrequencyCalculator.calculate(AlleleFrequencyCalculator.java:132) at org.broadinstitute.hellbender.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:153) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.calculateGenotypes(GenotypeGVCFsEngine.java:248) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.regenotypeVC(GenotypeGVCFsEngine.java:156) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFsEngine.callRegion(GenotypeGVCFsEngine.java:138) at org.broadinstitute.hellbender.tools.walkers.GenotypeGVCFs.apply(GenotypeGVCFs.java:324) at org.broadinstitute.hellbender.engine.VariantLocusWalker.lambda$traverse$0(VariantLocusWalker.java:137)
