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/e8/3e3d39f0664f31d4db697ffa24661d/1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/9ffc7f5fd8cc7bde311bae2bf0cbf1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/76/9ffc7f5fd8cc7bde311bae2bf0cbf1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/3e3d39f0664f31d4db697ffa24661d/1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1136_81F-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1136_81F-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1136_81F-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1136_81F-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1136_81F-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1136_81F-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_by_cycle_metrics
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:177000001, elapsed 11.7s, est remaining 221.5s, peak mem 2762MB, user 279.9s, sys 2.7s, output queue size 146
progress 10% @chr2:5000001, elapsed 19.7s, est remaining 177.3s, peak mem 3518MB, user 541.5s, sys 4.2s, output queue size 166
progress 15% @chr2:224000001, elapsed 28.1s, est remaining 159.0s, peak mem 3721MB, user 817.2s, sys 5.6s, output queue size 122
progress 20% @chr3:154000001, elapsed 36.7s, est remaining 146.7s, peak mem 3840MB, user 1080.8s, sys 6.5s, output queue size 141
progress 25% @chr4:136000001, elapsed 44.1s, est remaining 132.3s, peak mem 3975MB, user 1291.3s, sys 7.2s, output queue size 302
progress 30% @chr5:94000001, elapsed 49.5s, est remaining 115.5s, peak mem 4101MB, user 1461.1s, sys 7.9s, output queue size 464
progress 35% @chr6:70000001, elapsed 58.2s, est remaining 108.1s, peak mem 4423MB, user 1720.8s, sys 8.9s, output queue size 106
progress 40% @chr7:56000001, elapsed 66.9s, est remaining 100.3s, peak mem 4689MB, user 1986.3s, sys 10.1s, output queue size 195
progress 45% @chr8:66000001, elapsed 76.7s, est remaining 93.7s, peak mem 4689MB, user 2269.6s, sys 11.1s, output queue size 204
progress 50% @chr9:88000001, elapsed 83.9s, est remaining 83.9s, peak mem 4809MB, user 2516.0s, sys 11.9s, output queue size 187
progress 55% @chr10:104000001, elapsed 94.6s, est remaining 77.4s, peak mem 5348MB, user 2819.2s, sys 12.9s, output queue size 348
progress 60% @chr12:2000001, elapsed 106.6s, est remaining 71.1s, peak mem 5692MB, user 3160.8s, sys 13.8s, output queue size 260
progress 65% @chr13:24000001, elapsed 116.8s, est remaining 62.9s, peak mem 5865MB, user 3491.3s, sys 14.8s, output queue size 216
progress 70% @chr14:36000001, elapsed 122.6s, est remaining 52.5s, peak mem 5872MB, user 3641.9s, sys 15.3s, output queue size 377
progress 75% @chr16:42000001, elapsed 134.2s, est remaining 44.7s, peak mem 6162MB, user 3999.9s, sys 16.4s, output queue size 531
progress 80% @chr18:9000001, elapsed 151.3s, est remaining 37.8s, peak mem 6344MB, user 4512.7s, sys 17.9s, output queue size 280
progress 85% @chr20:25000001, elapsed 168.3s, est remaining 29.7s, peak mem 6344MB, user 5070.0s, sys 19.5s, output queue size 80
progress 90% @chrX:19000001, elapsed 177.1s, est remaining 19.7s, peak mem 6344MB, user 5406.3s, sys 20.7s, output queue size 121
progress 95% @chrY:54000001, elapsed 184.4s, est remaining 9.7s, peak mem 6344MB, user 5607.0s, sys 21.8s, output queue size 240
progress 100% @chrX:67000001, elapsed 198.5s, est remaining 0.0s, peak mem 6344MB, user 5791.5s, sys 22.6s, 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: 63239640700
reads: 1187143287
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1019.926 user 18.210 sys 1038.452 real
done: 1 calls 0.084 user 0.000 sys 0.091 real
exec_no_coor: 1 calls 0.015 user 0.015 sys 0.042 real
execute: 1 calls 0.002 user 0.005 sys 198.610 real
idle: 409 calls 0.166 user 0.000 sys 372.227 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 6652481536 mem 5793.813 user 22.938 sys 199.871 real