QUAL scores being returned as "." in output from CombineGVCFs
REQUIRED for all errors and issues:
a) GATK version used: GATK v4.3.0.0, HTSJDK Version: 3.0.1, Picard Version: 2.27.5
b) Exact command used:
gatk CombineGVCFs \
-R "$REFERENCE" \
--variant gvcf.list \
-O cohort.g.vcf.gz
c) Entire program log:
Using GATK jar /gpfs/home/jjt122/miniconda3/envs/gatk4/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 /gpfs/home/jjt122/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar CombineGVCFs -R /gpfs/home/jjt122/BDGenomics/Utpals_Projects/Mito_BD/JEL423_mtDNA.fasta --variant gvcf.list -O cohort.g.vcf.gz
13:37:27.972 INFO NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/gpfs/home/jjt122/miniconda3/envs/gatk4/share/gatk4-4.3.0.0-0/gatk-package-4.3.0.0-local.jar!/com/intel/gkl/native/libgkl_compression.so
13:37:28.099 INFO CombineGVCFs - ------------------------------------------------------------
13:37:28.099 INFO CombineGVCFs - The Genome Analysis Toolkit (GATK) v4.3.0.0
13:37:28.099 INFO CombineGVCFs - For support and documentation go to https://software.broadinstitute.org/gatk/
13:37:28.099 INFO CombineGVCFs - Executing as jjt122@himem-002.local on Linux v3.10.0-693.5.2.el7.x86_64 amd64
13:37:28.099 INFO CombineGVCFs - Java runtime: OpenJDK 64-Bit Server VM v11.0.15-internal+0-adhoc..src
13:37:28.100 INFO CombineGVCFs - Start Date/Time: October 6, 2023 at 1:37:27 PM CDT
13:37:28.100 INFO CombineGVCFs - ------------------------------------------------------------
13:37:28.100 INFO CombineGVCFs - ------------------------------------------------------------
13:37:28.100 INFO CombineGVCFs - HTSJDK Version: 3.0.1
13:37:28.100 INFO CombineGVCFs - Picard Version: 2.27.5
13:37:28.101 INFO CombineGVCFs - Built for Spark Version: 2.4.5
13:37:28.101 INFO CombineGVCFs - HTSJDK Defaults.COMPRESSION_LEVEL : 2
13:37:28.101 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
13:37:28.101 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
13:37:28.101 INFO CombineGVCFs - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
13:37:28.101 INFO CombineGVCFs - Deflater: IntelDeflater
13:37:28.101 INFO CombineGVCFs - Inflater: IntelInflater
13:37:28.101 INFO CombineGVCFs - GCS max retries/reopens: 20
13:37:28.101 INFO CombineGVCFs - Requester pays: disabled
13:37:28.101 INFO CombineGVCFs - Initializing engine
13:37:28.246 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6252317.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.252 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.261 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375433.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.262 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.268 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375434.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.269 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.274 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375435.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.275 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.280 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375436.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.281 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.286 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375437.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.287 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.291 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375438.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.294 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.298 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375439.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.299 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.303 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375440.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.304 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.308 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375441.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.309 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.313 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375442.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.314 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.318 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375443.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.319 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.323 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375444.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.324 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.327 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375445.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.329 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.332 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375446.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.348 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.359 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375447.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.360 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.364 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375448.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.365 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.368 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375449.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.369 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.373 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375450.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.374 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.378 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375453.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.379 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.382 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375454.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.383 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.387 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375455.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.388 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.391 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375456.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.392 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.395 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375457.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.396 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.399 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375458.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.400 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.403 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375459.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.404 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.407 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375460.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.408 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.411 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375461.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.412 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.415 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375462.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.416 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.419 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375463.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.420 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.423 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375464.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.424 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.427 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375465.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.428 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.431 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375466.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.432 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.435 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375467.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.436 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.439 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375468.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.440 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.443 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375469.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.444 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.446 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375470.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.448 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.450 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375471.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.451 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.454 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375472.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.455 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.458 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375473.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.459 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.461 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375474.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.462 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.465 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375475.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.466 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.469 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375476.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.470 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.473 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375477.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.473 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.476 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375478.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.477 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.479 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375479.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.480 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.483 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375480.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.484 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.487 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375481.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.488 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.491 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375482.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.491 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.494 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375483.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.495 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.498 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375484.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.499 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.502 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375485.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.503 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.506 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375486.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.507 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.509 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375487.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.510 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.513 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375488.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.514 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.517 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375489.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.518 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.520 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375490.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.521 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.524 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375491.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.525 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.527 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375492.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.528 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.530 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375493.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.531 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.534 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375494.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.535 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.537 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375495.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.538 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.541 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375496.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.542 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.544 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375497.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.545 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.548 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375498.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.549 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.551 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375499.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.552 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.555 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375500.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.556 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.558 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375501.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.559 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.562 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375502.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.563 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.566 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375503.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.567 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.569 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375504.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.570 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.572 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375505.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.573 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.576 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375506.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.577 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.579 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375507.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.580 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.583 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375508.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.584 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.586 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375509.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.587 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.590 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375510.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.591 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.596 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375511.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.597 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.600 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375512.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.601 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.604 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375513.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.605 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.608 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375514.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.609 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.611 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375515.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.613 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.615 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375516.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.616 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.619 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375517.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.620 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.623 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375518.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.624 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.627 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375519.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.628 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.631 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375520.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.632 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.635 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375521.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.636 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.638 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375522.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.640 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.643 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375523.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.645 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.647 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375524.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.649 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.651 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375525.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.653 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.656 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375526.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.660 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375527.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.662 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.665 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375528.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.666 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.669 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375529.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.671 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.674 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375530.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.699 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.702 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375531.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.706 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375532.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.707 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.709 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375533.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.710 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.712 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375534.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.714 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.716 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375535.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.717 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.719 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375536.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.720 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.722 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375537.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.723 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.726 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375538.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.726 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.729 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375539.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.730 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.732 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375540.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.733 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.735 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375541.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.736 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.738 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375542.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.740 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.742 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375543.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.746 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375544.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.750 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375545.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.754 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375546.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.756 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.758 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375547.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.760 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.762 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375548.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.766 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375549.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.770 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375550.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.774 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375551.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.775 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.777 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375552.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.778 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.781 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375553.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.782 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.785 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375554.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.785 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.788 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375555.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.789 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.791 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375556.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.792 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.794 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375557.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.795 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.797 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375558.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.798 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.800 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375559.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.800 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.803 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375560.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.803 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.806 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375561.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.807 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.809 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375562.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.809 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.812 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375563.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.813 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.815 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375564.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.817 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.819 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375565.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.822 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375566.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.824 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.826 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375567.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.830 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375568.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.830 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.832 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375569.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.833 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.835 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375570.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.836 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.838 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375571.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.840 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.842 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375572.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.843 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.845 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375573.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.861 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.864 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375574.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.865 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.867 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375575.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.868 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.870 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375576.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.871 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.873 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375577.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.874 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.876 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375578.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.877 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.879 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375579.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.881 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.883 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375580.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.887 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375581.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.891 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375582.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.895 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375583.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.898 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375584.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.902 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375585.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.906 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375586.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.907 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.909 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375587.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.911 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.913 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6375588.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.914 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.916 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378403.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.917 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.919 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378404.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.920 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.922 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378405.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.923 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.925 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378406.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.926 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.929 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378407.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.929 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.931 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378408.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.932 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.934 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378409.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.935 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.937 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378410.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.938 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.940 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378412.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.941 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.943 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378413.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.944 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.946 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378414.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.947 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.949 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378415.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.950 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.952 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378416.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.953 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.955 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378417.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.956 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.958 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378418.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.959 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.961 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378419.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.962 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.964 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378420.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.965 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.967 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378421.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.968 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.970 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378422.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.971 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.973 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378423.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.974 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.976 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378424.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.976 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.978 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378426.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.979 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.981 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378427.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.982 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.984 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378428.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.985 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.987 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378429.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.987 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.989 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378436.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.990 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.992 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378448.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.993 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.995 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/SRR6378449.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.996 WARN IntelInflater - Zero Bytes Written : 0
13:37:28.997 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM121_S17_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:28.998 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.000 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM125_S18_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.001 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.003 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM128_S19_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.004 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.006 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM15_S1_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.007 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.009 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM20_S2_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.010 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.012 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM26_S3_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.013 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.015 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM32_S4_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.016 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.018 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM33_S5_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.034 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.037 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM41_S6_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.038 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.040 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM46_S7_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.042 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.044 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM48_S20_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.045 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.047 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM63_S21_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.050 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM81_S8_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.051 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.053 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM88_S9_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.053 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.055 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM90_S10_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.056 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.058 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM91_S11_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.059 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.061 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM92_S12_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.062 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.064 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM93_S13_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.065 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.067 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM94_S14_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.068 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.070 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM95_S15_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.071 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.073 INFO FeatureManager - Using codec VCFCodec to read file file:///gpfs/home/jjt122/BDGenomics/Utpals_Projects/Results/Mito/bam1/temp-gvcf/TM96_S16_L001.sorted.dedup.q20.bam.g.vcf.gz
13:37:29.074 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.078 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.080 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.082 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.083 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.085 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.086 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.087 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.089 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.091 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.092 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.094 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.096 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.097 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.099 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.100 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.102 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.104 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.105 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.107 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.109 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.111 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.112 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.114 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.115 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.117 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.118 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.120 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.122 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.123 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.125 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.127 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.128 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.130 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.131 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.133 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.135 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.136 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.138 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.139 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.141 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.142 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.144 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.145 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.147 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.148 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.150 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.151 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.153 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.155 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.156 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.158 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.159 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.176 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.178 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.180 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.181 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.183 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.184 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.185 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.186 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.188 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.189 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.190 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.192 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.193 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.195 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.196 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.198 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.199 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.201 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.202 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.203 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.205 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.206 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.208 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.209 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.210 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.212 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.213 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.215 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.216 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.217 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.219 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.220 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.221 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.223 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.225 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.226 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.228 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.230 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.232 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.234 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.238 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.240 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.243 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.245 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.248 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.250 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.251 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.253 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.254 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.256 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.257 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.259 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.260 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.261 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.263 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.272 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.274 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.283 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.284 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.286 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.288 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.290 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.291 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.292 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.294 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.295 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.297 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.298 WARN IntelInflater - Zero Bytes Written : 0
13:37:29.300 WARN IntelInflater - Zero Bytes Written : 0
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13:37:29.866 INFO CombineGVCFs - Done initializing engine
13:37:29.891 INFO ProgressMeter - Starting traversal
13:37:29.892 INFO ProgressMeter - Current Locus Elapsed Minutes Variants Processed Variants/Minute
13:37:29.894 WARN IntelInflater - Zero Bytes Written : 0
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13:37:30.208 WARN ReferenceConfidenceVariantContextMerger - Detected invalid annotations: When trying to merge variant contexts at location DS022322.1mtDNA:31 the annotation MLEAC=[1, 0] was not a numerical value and was ignored
13:37:40.001 INFO ProgressMeter - DS022322.1mtDNA:48196 0.2 87000 516371.6
13:37:50.154 INFO ProgressMeter - DS022322.1mtDNA:82177 0.3 222000 657420.7
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13:38:00.184 INFO ProgressMeter - DS022322.1mtDNA:153578 0.5 302000 598177.7
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13:38:03.346 INFO ProgressMeter - DS022322.1mtDNA:175267 0.6 323966 581035.5
13:38:03.346 INFO ProgressMeter - Traversal complete. Processed 323966 total variants in 0.6 minutes.
13:38:03.359 INFO CombineGVCFs - Shutting down engine
[October 6, 2023 at 1:38:03 PM CDT] org.broadinstitute.hellbender.tools.walkers.CombineGVCFs done. Elapsed time: 0.59 minutes.
Runtime.totalMemory()=2147483648
Hi, I am running into an issue while combining multiple gvcf files using CombineGVCFs. Specifically, variant quality scores in the combined vcf are all being converted to ".", even when they have a score in the original vcf. Please see example in screenshots below where the QUAL score for position 14532 is 411.60 in the individual but is a "." in the combined vcf.
I would appreciate any feedback on what happens to QUAL scores when you merge vcfs using CombineGVCFs and whether what I am seeing is a bug.
Thank you in advance!
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Hi Utpal Smart
When GVCF files are combined to create a multisample GVCF file certain parameters are removed for future recalculation and recalculating those parameters require GenotypeGVCFs tool to run on your combined file. When you run the tool to get genotyped sites in a regular multisample VCF you will get your qual values as well as calls in regular spots.
The behavior you observe is the normal behavior of our tools.
I hope this helps.
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Hi Gökalp Çelik ,
Thanks for that response. So, if wanted to filter variants by qual scores, I would do it after running GenotypeVCFs on the combined gvcf first?
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Hi again.
Yes exactly. You need to run GenotypeGVCFs first to get your genotypes and scores calculated. Then you may use whatever filtering tool to cleanup your variants.
Regards.
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Perfect, thank you for that prompt clarification. One last related question: does the "WARN IntelInflater - Zero Bytes Written: 0" in the output indicate issues with combining gvcfs? I can open a new post about this if that is more appropriate.
Thanks.
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That warning is not an error message. It is the regular behavior of the tool indicating that there were zero instances where tool was used to write 0 bytes as output. It will not affect your results and your output should be ok.
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Good to know and thank you for those answers Gökalp Çelik !
Regards,
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