Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/24085c7efd571d6d80136fbf0eacad/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/24085c7efd571d6d80136fbf0eacad/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/3ff9499941a6df5e9cecb065774346/Sig_18_Blood.recalibrated.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ba/3ff9499941a6df5e9cecb065774346/Sig_18_Blood.recalibrated.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz ==> STAGING COMPLETE (9 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr1_69091-70008.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:18634302, elapsed 0.1s, est remaining 1.1s, peak mem 78MB, user 0.0s, sys 0.2s, output queue size 2211 progress 10% @chr1:37764961, elapsed 0.1s, est remaining 1.1s, peak mem 85MB, user 0.1s, sys 0.3s, output queue size 1904 progress 15% @chr1:65405870, elapsed 0.2s, est remaining 1.1s, peak mem 91MB, user 0.1s, sys 0.5s, output queue size 4628 progress 20% @chr1:113837590, elapsed 0.3s, est remaining 1.0s, peak mem 103MB, user 0.1s, sys 0.6s, output queue size 7390 progress 25% @chr1:155248050, elapsed 0.3s, est remaining 0.9s, peak mem 111MB, user 0.1s, sys 0.8s, output queue size 9733 progress 30% @chr1:179348844, elapsed 0.4s, est remaining 0.8s, peak mem 123MB, user 0.2s, sys 0.9s, output queue size 12229 progress 35% @chr1:209796348, elapsed 0.4s, est remaining 0.8s, peak mem 129MB, user 0.2s, sys 1.1s, output queue size 14635 progress 40% @chr1:247100374, elapsed 0.5s, est remaining 0.7s, peak mem 139MB, user 0.2s, sys 1.2s, output queue size 17050 progress 45% @chr2:32549313, elapsed 0.5s, est remaining 0.6s, peak mem 148MB, user 0.2s, sys 1.4s, output queue size 19332 progress 50% @chr2:74460221, elapsed 0.6s, est remaining 0.6s, peak mem 159MB, user 0.3s, sys 1.5s, output queue size 21819 progress 55% @chr2:113499257, elapsed 0.6s, est remaining 0.5s, peak mem 168MB, user 0.3s, sys 1.7s, output queue size 24351 progress 60% @chr2:171006474, elapsed 0.7s, est remaining 0.4s, peak mem 181MB, user 0.3s, sys 1.8s, output queue size 27050 progress 65% @chr2:202757213, elapsed 0.7s, est remaining 0.4s, peak mem 189MB, user 0.3s, sys 2.0s, output queue size 29320 progress 70% @chr2:233772261, elapsed 0.8s, est remaining 0.3s, peak mem 199MB, user 0.4s, sys 2.2s, output queue size 31796 progress 75% @chr3:25612515, elapsed 0.8s, est remaining 0.3s, peak mem 208MB, user 0.4s, sys 2.3s, output queue size 34020 progress 80% @chr3:49807736, elapsed 0.9s, est remaining 0.2s, peak mem 217MB, user 0.5s, sys 2.4s, output queue size 36494 progress 85% @chr3:101859272, elapsed 0.9s, est remaining 0.2s, peak mem 223MB, user 0.5s, sys 2.6s, output queue size 39129 progress 90% @chr3:140546515, elapsed 1.0s, est remaining 0.1s, peak mem 238MB, user 0.5s, sys 2.7s, output queue size 41739 progress 95% @chr3:188524665, elapsed 1.0s, est remaining 0.1s, peak mem 249MB, user 0.5s, sys 2.8s, output queue size 44140 progress 100% @chr4:23824463, elapsed 1.1s, est remaining 0.0s, peak mem 258MB, user 0.6s, sys 2.9s, output queue size 46371 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.83 cpu vendor: GenuineIntel signature: 000a06d1 features: bfebfbff 7ffefbff extended: f3bfb7ef fb417ffe amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) 6975P-C threads: 12 max 192 algo: Haplotyper license: sentieon:Haplotyper=12 input file size: 74586797 output file size: 22307 reads: 1001133 contig: 49651 intervals 9000373 bases active: 100735 calls 0.000 user 0.005 sys 0.019 real advance: 51084 calls 0.000 user 0.006 sys 0.027 real calc: 100735 calls 0.000 user 0.000 sys 0.019 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.002 user 0.001 sys 3.075 real fetch: 100735 calls 0.002 user 0.002 sys 0.019 real fetch_ref: 100735 calls 0.044 user 0.048 sys 0.438 real idle: 51 calls 0.003 user 0.018 sys 36.397 real init: 1 calls 0.039 user 0.004 sys 0.051 real region: 100735 calls 0.001 user 0.000 sys 0.021 real tracker: 100735 calls 0.012 user 0.004 sys 0.109 real overall: 273940480 mem 1.241 user 5.605 sys 4.212 real ls: cannot access '*.g.vcf.gz': No such file or directory ls: cannot access '*.g.vcf.gz.tbi': No such file or directory