Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/1136_4Z5-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/4b/8a67a4930c75ff0573fec03e4ea2c8/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/8d35f2b15b1928f0e620f9cbab5ae1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/8d35f2b15b1928f0e620f9cbab5ae1/.command.run
  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_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam --algo AlignmentStat 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.alignment_summary_metrics --algo InsertSizeMetricAlgo 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.insert_size_metrics --algo QualDistribution 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.quality_distribution_metrics --algo BaseDistributionByCycle 1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.sentieon.base_distribution_by_cycle_metrics --algo MeanQualityByCycle 1136_4Z5-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 10.5s, est remaining 199.3s, peak mem 2715MB, user 237.1s, sys 2.6s, output queue size 150
progress 10% @chr1:243000001, elapsed 20.5s, est remaining 184.1s, peak mem 4192MB, user 567.2s, sys 4.6s, output queue size 117
progress 15% @chr3:11000001, elapsed 34.2s, est remaining 194.0s, peak mem 5680MB, user 956.2s, sys 6.6s, output queue size 124
progress 20% @chr3:174000001, elapsed 42.5s, est remaining 170.1s, peak mem 5821MB, user 1226.8s, sys 7.6s, output queue size 283
progress 25% @chr4:129000001, elapsed 49.6s, est remaining 148.7s, peak mem 5874MB, user 1447.2s, sys 8.5s, output queue size 444
progress 30% @chr5:56000001, elapsed 55.2s, est remaining 128.8s, peak mem 5908MB, user 1609.1s, sys 9.1s, output queue size 606
progress 35% @chr6:86000001, elapsed 65.4s, est remaining 121.5s, peak mem 6263MB, user 1852.8s, sys 9.7s, output queue size 767
progress 40% @chr7:65000001, elapsed 78.3s, est remaining 117.5s, peak mem 7532MB, user 2208.0s, sys 10.9s, output queue size 928
progress 45% @chr8:74000001, elapsed 96.0s, est remaining 117.3s, peak mem 7759MB, user 2676.6s, sys 12.4s, output queue size 1090
progress 50% @chr9:87000001, elapsed 108.9s, est remaining 108.9s, peak mem 8020MB, user 2998.7s, sys 13.2s, output queue size 1252
progress 55% @chr10:101000001, elapsed 120.3s, est remaining 98.4s, peak mem 8741MB, user 3487.6s, sys 14.7s, output queue size 668
progress 60% @chr11:134000001, elapsed 133.7s, est remaining 89.1s, peak mem 9287MB, user 3866.2s, sys 15.7s, output queue size 830
progress 65% @chr12:111000001, elapsed 146.7s, est remaining 79.0s, peak mem 12306MB, user 4230.2s, sys 16.5s, output queue size 992
progress 70% @chr14:83000001, elapsed 156.9s, est remaining 67.2s, peak mem 12440MB, user 4680.8s, sys 17.6s, output queue size 970
progress 75% @chr16:42000001, elapsed 170.7s, est remaining 56.9s, peak mem 12737MB, user 5040.7s, sys 18.5s, output queue size 1132
progress 80% @chr18:25000001, elapsed 189.6s, est remaining 47.4s, peak mem 13870MB, user 5578.4s, sys 19.8s, output queue size 1294
progress 85% @chr19:52000001, elapsed 208.0s, est remaining 36.7s, peak mem 13952MB, user 6154.3s, sys 20.8s, output queue size 1456
progress 90% @chr22:24000001, elapsed 219.2s, est remaining 24.4s, peak mem 14002MB, user 6572.4s, sys 21.6s, output queue size 1618
progress 95% @chrY:55000001, elapsed 225.7s, est remaining 11.9s, peak mem 14002MB, user 6747.9s, sys 22.1s, output queue size 1780
progress 100% @chr7:55000001, elapsed 2560.5s, est remaining 0.0s, peak mem 19879MB, user 9346.9s, sys 72.3s, output queue size 5204
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: 71921241447
reads: 1527741288
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 1253.001 user 35.000 sys 1284.469 real
done: 1 calls 0.070 user 0.000 sys 0.072 real
exec_no_coor: 1 calls 0.028 user 0.038 sys 0.079 real
execute: 1 calls 0.003 user 0.001 sys 2561.398 real
idle: 70037 calls 1.991 user 0.691 sys 70014.429 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 20844789760 mem 9350.876 user 73.700 sys 2563.008 real