Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0a/33b1c3ef876f67c1658eae3a9e8968/1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/9bd82272a56bbbd542ab68da5e2057/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7d/9bd82272a56bbbd542ab68da5e2057/.command.run
  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/0a/33b1c3ef876f67c1658eae3a9e8968/1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1047_JG-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1047_JG-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:188000001, elapsed 33.3s, est remaining 632.9s, peak mem 8127MB, user 796.8s, sys 9.4s, output queue size 146
progress 10% @chr2:94000001, elapsed 63.6s, est remaining 572.6s, peak mem 11511MB, user 1693.7s, sys 14.7s, output queue size 143
progress 15% @chr3:13000001, elapsed 97.6s, est remaining 553.1s, peak mem 12914MB, user 2728.1s, sys 21.3s, output queue size 188
progress 20% @chr3:175000001, elapsed 128.1s, est remaining 512.5s, peak mem 13659MB, user 3609.0s, sys 25.4s, output queue size 283
progress 25% @chr4:134000001, elapsed 155.0s, est remaining 465.0s, peak mem 13956MB, user 4518.9s, sys 28.2s, output queue size 302
progress 30% @chr5:83000001, elapsed 175.4s, est remaining 409.2s, peak mem 14608MB, user 5132.8s, sys 30.0s, output queue size 464
progress 35% @chr6:86000001, elapsed 204.5s, est remaining 379.8s, peak mem 14684MB, user 5970.8s, sys 32.9s, output queue size 625
progress 40% @chr7:66000001, elapsed 237.6s, est remaining 356.3s, peak mem 15194MB, user 6870.1s, sys 36.2s, output queue size 786
progress 45% @chr8:67000001, elapsed 276.7s, est remaining 338.2s, peak mem 15388MB, user 7899.9s, sys 38.5s, output queue size 948
progress 50% @chr9:87000001, elapsed 309.7s, est remaining 309.7s, peak mem 15995MB, user 8810.8s, sys 41.3s, output queue size 1110
progress 55% @chr10:96000001, elapsed 343.8s, est remaining 281.3s, peak mem 16133MB, user 10110.3s, sys 43.9s, output queue size 527
progress 60% @chr11:134000001, elapsed 377.9s, est remaining 251.9s, peak mem 16133MB, user 11059.1s, sys 45.6s, output queue size 689
progress 65% @chr12:111000001, elapsed 418.3s, est remaining 225.2s, peak mem 16272MB, user 12275.6s, sys 47.6s, output queue size 672
progress 70% @chr14:76000001, elapsed 439.1s, est remaining 188.2s, peak mem 16272MB, user 12966.8s, sys 48.9s, output queue size 833
progress 75% @chr16:42000001, elapsed 478.1s, est remaining 159.4s, peak mem 16289MB, user 14122.8s, sys 51.3s, output queue size 995
progress 80% @chr17:82000001, elapsed 533.0s, est remaining 133.3s, peak mem 16447MB, user 15567.4s, sys 54.2s, output queue size 1157
progress 85% @chr8:32000001, elapsed 582.4s, est remaining 102.8s, peak mem 16657MB, user 17276.2s, sys 57.1s, output queue size 1319
progress 90% @chrX:18000001, elapsed 613.1s, est remaining 68.1s, peak mem 16904MB, user 18336.3s, sys 59.4s, output queue size 947
progress 95% @chrY:55000001, elapsed 636.5s, est remaining 33.5s, peak mem 16953MB, user 18852.5s, sys 60.8s, output queue size 1109
progress 100% @chrX:67000001, elapsed 712.0s, est remaining 0.0s, peak mem 17120MB, user 20119.0s, sys 63.2s, output queue size 3540
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: 1f8bfbff fffab20b
  extended: f1bf27eb 1b407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 192
algo: AlignmentStat InsertSizeMetricAlgo QualDistribution BaseDistributionByCycle MeanQualityByCycle
license: sentieon:Metrics=31
input file size: 140423331250
reads: 3098808471
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 2483.923 user 55.174 sys 2521.437 real
done: 1 calls 0.067 user 0.001 sys 0.074 real
exec_no_coor: 1 calls 0.084 user 0.063 sys 0.166 real
execute: 1 calls 0.001 user 0.001 sys 712.167 real
idle: 1951 calls 0.212 user 0.003 sys 1923.341 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 17952018432 mem 20121.643 user 64.105 sys 713.922 real