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/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b4859e2819e5c08f9ce4cd4fa95b10/HCC1395_BL.recalibrated.bam Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/1e2509459667994c29017f1c427d25/.command.sh Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz.tbi Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/b4859e2819e5c08f9ce4cd4fa95b10/HCC1395_BL.recalibrated.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/1e2509459667994c29017f1c427d25/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict ==> STAGING COMPLETE (14 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:113682112, elapsed 1.4s, est remaining 25.7s, peak mem 142MB, user 12.4s, sys 1.7s, output queue size 4 progress 10% @chr2:3643344, elapsed 2.6s, est remaining 23.8s, peak mem 143MB, user 24.2s, sys 3.4s, output queue size 6 progress 15% @chr2:178600754, elapsed 4.0s, est remaining 22.7s, peak mem 143MB, user 36.6s, sys 5.0s, output queue size 12 progress 20% @chr3:57489409, elapsed 5.3s, est remaining 21.3s, peak mem 144MB, user 48.6s, sys 6.4s, output queue size 0 progress 25% @chr4:70598256, elapsed 6.7s, est remaining 20.2s, peak mem 144MB, user 61.8s, sys 7.9s, output queue size 8 progress 30% @chr5:135571753, elapsed 8.2s, est remaining 19.1s, peak mem 146MB, user 75.2s, sys 9.5s, output queue size 4 progress 35% @chr6:104957999, elapsed 9.5s, est remaining 17.7s, peak mem 148MB, user 87.3s, sys 10.8s, output queue size 2 progress 40% @chr7:106284249, elapsed 10.9s, est remaining 16.4s, peak mem 148MB, user 100.0s, sys 12.4s, output queue size 5 progress 45% @chr8:143821497, elapsed 12.3s, est remaining 15.1s, peak mem 149MB, user 113.0s, sys 13.8s, output queue size 1 progress 50% @chr10:21514996, elapsed 13.7s, est remaining 13.7s, peak mem 151MB, user 126.1s, sys 15.0s, output queue size 13 progress 55% @chr11:34136878, elapsed 15.0s, est remaining 12.3s, peak mem 151MB, user 138.7s, sys 16.4s, output queue size 2 progress 60% @chr12:12718707, elapsed 16.3s, est remaining 10.9s, peak mem 152MB, user 150.4s, sys 18.0s, output queue size 10 progress 65% @chr13:32078734, elapsed 17.7s, est remaining 9.5s, peak mem 152MB, user 162.7s, sys 19.4s, output queue size 10 progress 70% @chr15:35381722, elapsed 19.0s, est remaining 8.1s, peak mem 152MB, user 175.4s, sys 20.8s, output queue size 2 progress 75% @chr16:28494582, elapsed 20.3s, est remaining 6.8s, peak mem 152MB, user 187.6s, sys 22.3s, output queue size 4 progress 80% @chr17:40034816, elapsed 21.8s, est remaining 5.4s, peak mem 153MB, user 201.2s, sys 23.7s, output queue size 3 progress 85% @chr19:1652201, elapsed 23.1s, est remaining 4.1s, peak mem 153MB, user 214.3s, sys 25.2s, output queue size 15 progress 90% @chr19:54630974, elapsed 24.5s, est remaining 2.7s, peak mem 154MB, user 226.9s, sys 26.5s, output queue size 2 progress 95% @chr22:32068396, elapsed 27.6s, est remaining 1.5s, peak mem 335MB, user 256.9s, sys 28.4s, output queue size 10 progress 100% @chrY:21542591, elapsed 28.8s, est remaining 0.0s, peak mem 335MB, user 267.8s, sys 29.8s, output queue size 507 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: AuthenticAMD signature: 00800f12 features: 178bfbff fed83203 extended: 209c01a9 00000000 amd bits: 2fd3fbff 00c001f3 brand: AMD EPYC 7571 threads: 12 max 64 algo: TNhaplotyper2 OrientationBias ContaminationModel license: sentieon:TNhaplotyper=12 input file size: 71721858 71692759 output file size: 46614 reads: 1501772 contig: 178193 intervals 76355618 bases "assemble": 183 calls 0.928 user 0.022 sys 0.889 real "assemble_addRead": 183 calls 0.010 user 0.000 sys 0.013 real "assemble_buildGraph": 422 calls 0.439 user 0.010 sys 0.392 real "assemble_computecigar": 264 calls 0.150 user 0.020 sys 0.177 real "assemble_kg_build_calcsize": 422 calls 0.207 user 0.010 sys 0.199 real "assemble_kg_build_clear": 573 calls 0.022 user 0.000 sys 0.016 real "assemble_kg_build_prepare": 844 calls 0.174 user 0.011 sys 0.193 real "assemble_kg_build_threading": 271 calls 0.212 user 0.000 sys 0.184 real "assemble_kg_op1": 271 calls 0.103 user 0.000 sys 0.102 real "assemble_kg_op2": 271 calls 0.020 user 0.000 sys 0.008 real "assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.008 real "assemble_sg_clean": 264 calls 0.054 user 0.000 sys 0.046 real "assemble_sg_create": 264 calls 0.038 user 0.001 sys 0.067 real "checkGraph": 183 calls 0.000 user 0.000 sys 0.001 real "findHaplotype": 183 calls 0.150 user 0.020 sys 0.185 real advance: 189104 calls 20.707 user 0.901 sys 32.703 real assemble_region: 183 calls 1.088 user 0.042 sys 1.091 real build_pileup: 70974 calls 0.692 user 0.060 sys 1.206 real build_stats: 71688 calls 4.704 user 0.243 sys 6.888 real build_variants: 142 calls 0.000 user 0.000 sys 0.002 real calc: 128670 calls 4.204 user 0.144 sys 6.977 real calc_region: 142 calls 4.316 user 0.034 sys 4.385 real call_region: 142 calls 0.090 user 0.010 sys 0.078 real clip_region: 325 calls 0.060 user 0.000 sys 0.055 real done: 1 calls 1.255 user 0.000 sys 1.259 real execute: 1 calls 0.003 user 0.011 sys 28.801 real fetch: 743546 calls 1.542 user 0.217 sys 2.116 real fetch_ref: 745688 calls 1.546 user 0.883 sys 5.079 real fetch_region: 183 calls 0.000 user 0.000 sys 0.014 real fetch_vcf: 189104 calls 59.458 user 3.056 sys 106.273 real idle: 47 calls 0.003 user 0.001 sys 26.400 real init: 1 calls 0.120 user 0.020 sys 0.142 real pairhmm: 472 calls 6.885 user 0.031 sys 6.858 real realign: 142 calls 0.561 user 0.009 sys 0.579 real region: 367297 calls 5.502 user 0.143 sys 5.771 real tracker: 367297 calls 0.813 user 0.166 sys 1.463 real trim_region: 183 calls 0.000 user 0.000 sys 0.004 real overall: 351891456 mem 300.649 user 42.618 sys 31.452 real