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-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam.bai
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/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/de5083cc160e4be0dda1dc9f445adc/.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-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260320_LH00527_0067_B23KGCJLT4__d7a6b981--20260322-105015/alignments/recalibrated/1029_01S-N1-BDNA-1_B23KGCJLT4_1/1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
Downloading: s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/daq/20260318_LH00519_0070_B23KFCWLT4__d7a6b981--20260320-092016/alignments/recalibrated/1029_01S-T1-TDNA-1_B23KFCWLT4_1/1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/de5083cc160e4be0dda1dc9f445adc/.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 1029_01S-N1-BDNA-1_B23KGCJLT4_1.recalibrated.bam -i 1029_01S-T1-TDNA-1_B23KFCWLT4_1.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo TNhaplotyper2 --tumor_sample 1029_01S-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_01S-N1-BDNA-1_B23KGCJLT4_1 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz 1029_01S.tnseq.vcf.gz --algo OrientationBias --tumor_sample 1029_01S-T1-TDNA-1_B23KFCWLT4_1 1029_01S.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample 1029_01S-T1-TDNA-1_B23KFCWLT4_1 --normal_sample 1029_01S-N1-BDNA-1_B23KGCJLT4_1 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments 1029_01S.tnseq.segments 1029_01S.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119911554, elapsed 143.1s, est remaining 2718.0s, peak mem 5984MB, user 1235.4s, sys 23.3s, output queue size 160
progress 10% @chr2:21001730, elapsed 368.3s, est remaining 3314.4s, peak mem 6741MB, user 2895.4s, sys 39.2s, output queue size 642
progress 15% @chr2:189743275, elapsed 589.1s, est remaining 3338.1s, peak mem 8252MB, user 4599.3s, sys 55.2s, output queue size 403
progress 20% @chr3:98784945, elapsed 769.4s, est remaining 3077.6s, peak mem 8252MB, user 6210.9s, sys 69.1s, output queue size 422
progress 25% @chr4:88462135, elapsed 916.8s, est remaining 2750.3s, peak mem 8252MB, user 7445.7s, sys 82.1s, output queue size 87
progress 30% @chr5:147509478, elapsed 1043.6s, est remaining 2435.1s, peak mem 8252MB, user 8456.2s, sys 93.7s, output queue size 198
progress 35% @chr6:131851142, elapsed 1359.3s, est remaining 2524.4s, peak mem 8252MB, user 10860.9s, sys 110.2s, output queue size 615
progress 40% @chr7:128866410, elapsed 1684.9s, est remaining 2527.4s, peak mem 8653MB, user 13171.4s, sys 127.2s, output queue size 1561
progress 45% @chr9:990041, elapsed 1959.5s, est remaining 2394.9s, peak mem 8700MB, user 15542.6s, sys 144.5s, output queue size 109
progress 50% @chr10:32845876, elapsed 2113.4s, est remaining 2113.4s, peak mem 8818MB, user 16884.2s, sys 158.2s, output queue size 69
progress 55% @chr11:47589821, elapsed 2310.2s, est remaining 1890.2s, peak mem 8818MB, user 18259.1s, sys 168.9s, output queue size 110
progress 60% @chr12:22512647, elapsed 2499.4s, est remaining 1666.3s, peak mem 9374MB, user 19742.7s, sys 182.6s, output queue size 638
progress 65% @chr13:49488290, elapsed 2678.7s, est remaining 1442.4s, peak mem 9374MB, user 21106.8s, sys 194.6s, output queue size 558
progress 70% @chr15:43160681, elapsed 3005.4s, est remaining 1288.0s, peak mem 9696MB, user 23907.7s, sys 208.2s, output queue size 454
progress 75% @chr16:30930073, elapsed 3153.5s, est remaining 1051.2s, peak mem 9825MB, user 25313.4s, sys 219.6s, output queue size 21
progress 80% @chr17:42581813, elapsed 3294.3s, est remaining 823.6s, peak mem 9841MB, user 26668.3s, sys 230.8s, output queue size 120