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/89/2eaa6e299df92fc7f7611cf65d4168/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c2b0eb611467aa29ca8c1489de19bf/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/c2b0eb611467aa29ca8c1489de19bf/.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/89/2eaa6e299df92fc7f7611cf65d4168/HCC1395_BL.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_BL.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:157000001, elapsed 0.1s, est remaining 2.4s, peak mem 78MB, user 0.2s, sys 3.0s, output queue size 4
progress 10% @chr2:69000001, elapsed 0.2s, est remaining 2.2s, peak mem 78MB, user 0.4s, sys 6.4s, output queue size 4
progress 15% @chr2:232000001, elapsed 0.4s, est remaining 2.0s, peak mem 78MB, user 0.7s, sys 9.6s, output queue size 3
progress 20% @chr3:152000001, elapsed 0.5s, est remaining 1.9s, peak mem 78MB, user 1.0s, sys 12.9s, output queue size 1
progress 25% @chr4:116000001, elapsed 0.6s, est remaining 1.7s, peak mem 78MB, user 1.2s, sys 16.2s, output queue size 1
progress 30% @chr5:88000001, elapsed 0.7s, est remaining 1.7s, peak mem 78MB, user 1.4s, sys 20.5s, output queue size 4
progress 35% @chr6:59000001, elapsed 0.9s, est remaining 1.7s, peak mem 78MB, user 1.6s, sys 26.5s, output queue size 7
progress 40% @chr7:49000001, elapsed 1.1s, est remaining 1.7s, peak mem 78MB, user 1.8s, sys 32.5s, output queue size 6
progress 45% @chr8:57000001, elapsed 1.3s, est remaining 1.6s, peak mem 78MB, user 2.0s, sys 38.6s, output queue size 8
progress 50% @chr9:75000001, elapsed 1.5s, est remaining 1.5s, peak mem 78MB, user 2.1s, sys 44.7s, output queue size 4
progress 55% @chr10:102000001, elapsed 1.7s, est remaining 1.4s, peak mem 78MB, user 2.4s, sys 50.6s, output queue size 8
progress 60% @chr11:114000001, elapsed 1.9s, est remaining 1.3s, peak mem 78MB, user 2.5s, sys 56.5s, output queue size 9
progress 65% @chr13:17000001, elapsed 2.1s, est remaining 1.1s, peak mem 78MB, user 2.7s, sys 62.4s, output queue size 3
progress 70% @chr14:62000001, elapsed 2.3s, est remaining 1.0s, peak mem 78MB, user 2.8s, sys 68.2s, output queue size 4
progress 75% @chr16:14000001, elapsed 2.5s, est remaining 0.8s, peak mem 78MB, user 3.0s, sys 74.1s, output queue size 8
progress 80% @chr18:2000001, elapsed 2.7s, est remaining 0.7s, peak mem 78MB, user 3.2s, sys 79.8s, output queue size 2
progress 85% @chr20:22000001, elapsed 2.9s, est remaining 0.5s, peak mem 78MB, user 3.4s, sys 85.6s, output queue size 4
progress 90% @chrX:29000001, elapsed 3.2s, est remaining 0.4s, peak mem 96MB, user 4.2s, sys 90.8s, output queue size 114
progress 95% @chrY:34000001, elapsed 3.4s, est remaining 0.2s, peak mem 126MB, user 4.6s, sys 97.4s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.8s, est remaining 0.0s, peak mem 171MB, user 5.2s, sys 106.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411649
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.008 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.274 user 23.257 sys 24.073 real
calc: 3219322 calls 0.347 user 17.821 sys 16.417 real
done: 1 calls 0.031 user 0.008 sys 0.047 real
execute: 1 calls 0.001 user 0.003 sys 3.812 real
fetch: 3219322 calls 0.346 user 17.250 sys 16.218 real
idle: 82 calls 0.005 user 0.026 sys 36.101 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220356608 mem 5.390 user 107.393 sys 4.872 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_BL.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_BL.md.score --metrics HCC1395_BL.md.metrics HCC1395_BL.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:163000001, elapsed 0.1s, est remaining 2.0s, peak mem 180MB, user 0.3s, sys 2.4s, output queue size 8
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.7s, peak mem 183MB, user 0.7s, sys 4.5s, output queue size 19
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.5s, peak mem 216MB, user 1.0s, sys 6.7s, output queue size 13
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.4s, peak mem 231MB, user 1.2s, sys 8.8s, output queue size 2
progress 25% @chr4:113000001, elapsed 0.4s, est remaining 1.3s, peak mem 240MB, user 1.4s, sys 11.1s, output queue size 10
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.2s, peak mem 246MB, user 1.7s, sys 13.2s, output queue size 12
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.1s, peak mem 252MB, user 1.9s, sys 15.4s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.7s, est remaining 1.0s, peak mem 255MB, user 2.2s, sys 17.6s, output queue size 1
progress 45% @chr8:55000001, elapsed 0.7s, est remaining 0.9s, peak mem 264MB, user 2.4s, sys 19.9s, output queue size 2
progress 50% @chr9:74000001, elapsed 0.8s, est remaining 0.8s, peak mem 267MB, user 2.6s, sys 22.1s, output queue size 6
progress 55% @chr10:96000001, elapsed 0.9s, est remaining 0.7s, peak mem 267MB, user 2.8s, sys 24.3s, output queue size 16
progress 60% @chr11:103000001, elapsed 1.0s, est remaining 0.7s, peak mem 270MB, user 3.0s, sys 26.6s, output queue size 20
progress 65% @chr13:16000001, elapsed 1.1s, est remaining 0.6s, peak mem 273MB, user 3.2s, sys 28.9s, output queue size 17
progress 70% @chr14:86000001, elapsed 1.2s, est remaining 0.5s, peak mem 273MB, user 3.4s, sys 32.9s, output queue size 23
progress 75% @chr15:84000001, elapsed 1.4s, est remaining 0.5s, peak mem 276MB, user 3.7s, sys 38.0s, output queue size 31
progress 80% @chr18:19000001, elapsed 1.6s, est remaining 0.4s, peak mem 276MB, user 4.0s, sys 44.2s, output queue size 20
progress 85% @chr20:40000001, elapsed 1.8s, est remaining 0.3s, peak mem 279MB, user 4.4s, sys 51.0s, output queue size 17
progress 90% @chrX:31000001, elapsed 2.2s, est remaining 0.2s, peak mem 516MB, user 6.9s, sys 55.7s, output queue size 114
progress 95% @chrY:24000001, elapsed 2.4s, est remaining 0.1s, peak mem 522MB, user 10.8s, sys 61.5s, output queue size 240
progress 100% @chr21:41000001, elapsed 3.5s, est remaining 0.0s, peak mem 534MB, user 13.5s, sys 68.4s, output queue size 3664
library HCC1395_BL:
chimeric_paired 873
duped 146553
duped_chimeric_paired 2
duped_paired 146548
duped_unpaired 5
optical_dup 4835
paired 999974
reads 1001089
secondary_supplementary 1097
unmapped 9
unpaired 9
optical dup clusters 4702, maxdup 7, total optical dup pairs 4835
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411649
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.001 user 0.029 sys 0.061 real
MateInfoByVcf::load: 25531 calls 3.854 user 1.245 sys 4.208 real
MateInfoByVcf::parse_events: 25531 calls 3.795 user 1.107 sys 3.931 real
advance: 3219322 calls 1.147 user 8.569 sys 10.071 real
calc: 3219322 calls 4.688 user 24.658 sys 30.204 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.005 user 0.002 sys 3.598 real
fetch: 3219322 calls 0.431 user 8.575 sys 8.310 real
find_pairEnds: 25531 calls 0.268 user 0.043 sys 0.387 real
idle: 984 calls 0.044 user 0.171 sys 57.521 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 25531 calls 0.856 user 0.199 sys 1.519 real
vcfadvance: 25531 calls 0.022 user 0.136 sys 0.073 real
write: 3219322 calls 2.546 user 8.156 sys 10.938 real
overall: 559992832 mem 13.997 user 69.757 sys 4.619 real