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/15/77f20302c0bbfeed972fa5de3d1b5d/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/81816b54ab7484624d9fee8b6881d3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/81816b54ab7484624d9fee8b6881d3/.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/15/77f20302c0bbfeed972fa5de3d1b5d/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% @chr1:149000001, elapsed 0.1s, est remaining 2.3s, peak mem 78MB, user 0.2s, sys 2.9s, output queue size 26
progress 10% @chr2:88000001, elapsed 0.2s, est remaining 2.1s, peak mem 78MB, user 0.4s, sys 6.1s, output queue size 17
progress 15% @chr2:238000001, elapsed 0.3s, est remaining 1.9s, peak mem 78MB, user 0.7s, sys 9.1s, output queue size 18
progress 20% @chr3:160000001, elapsed 0.4s, est remaining 1.8s, peak mem 78MB, user 0.9s, sys 12.2s, output queue size 13
progress 25% @chr4:96000001, elapsed 0.5s, est remaining 1.6s, peak mem 78MB, user 1.2s, sys 15.2s, output queue size 32
progress 30% @chr5:68000001, elapsed 0.7s, est remaining 1.5s, peak mem 78MB, user 1.4s, sys 18.3s, output queue size 19
progress 35% @chr6:63000001, elapsed 0.8s, est remaining 1.5s, peak mem 78MB, user 1.8s, sys 22.5s, output queue size 28
progress 40% @chr7:14000001, elapsed 1.0s, est remaining 1.5s, peak mem 78MB, user 2.2s, sys 27.1s, output queue size 41
progress 45% @chr8:59000001, elapsed 1.1s, est remaining 1.4s, peak mem 78MB, user 2.6s, sys 31.8s, output queue size 25
progress 50% @chr9:75000001, elapsed 1.3s, est remaining 1.3s, peak mem 78MB, user 2.8s, sys 36.6s, output queue size 32
progress 55% @chr10:50000001, elapsed 1.5s, est remaining 1.2s, peak mem 78MB, user 3.0s, sys 41.3s, output queue size 45
progress 60% @chr12:9000001, elapsed 1.6s, est remaining 1.1s, peak mem 78MB, user 3.2s, sys 45.9s, output queue size 81
progress 65% @chr13:37000001, elapsed 1.8s, est remaining 1.0s, peak mem 78MB, user 3.4s, sys 50.7s, output queue size 65
progress 70% @chr14:84000001, elapsed 2.0s, est remaining 0.8s, peak mem 78MB, user 3.7s, sys 55.5s, output queue size 86
progress 75% @chr16:36000001, elapsed 2.1s, est remaining 0.7s, peak mem 78MB, user 3.8s, sys 60.7s, output queue size 39
progress 80% @chr18:23000001, elapsed 2.3s, est remaining 0.6s, peak mem 78MB, user 4.2s, sys 65.7s, output queue size 58
progress 85% @chr20:46000001, elapsed 2.5s, est remaining 0.4s, peak mem 78MB, user 4.5s, sys 70.7s, output queue size 62
progress 90% @chrX:12000001, elapsed 2.7s, est remaining 0.3s, peak mem 87MB, user 5.0s, sys 76.3s, output queue size 114
progress 95% @chrY:53000001, elapsed 3.0s, est remaining 0.2s, peak mem 123MB, user 5.4s, sys 82.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.4s, est remaining 0.0s, peak mem 174MB, user 6.3s, sys 92.1s, 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: 50411664
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.010 user 0.047 sys 0.062 real
VcfLineRecordHelper::sort: 30 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.334 user 19.462 sys 21.740 real
calc: 3219322 calls 0.300 user 14.796 sys 15.145 real
done: 1 calls 0.010 user 0.047 sys 0.062 real
execute: 1 calls 0.003 user 0.006 sys 3.430 real
fetch: 3219322 calls 0.457 user 14.459 sys 15.210 real
idle: 83 calls 0.010 user 0.054 sys 37.601 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 229371904 mem 6.441 user 92.832 sys 4.490 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% @chr1:162000001, elapsed 0.1s, est remaining 2.1s, peak mem 174MB, user 0.2s, sys 2.6s, output queue size 2
progress 10% @chr2:67000001, elapsed 0.2s, est remaining 1.9s, peak mem 192MB, user 0.4s, sys 5.3s, output queue size 11
progress 15% @chr2:233000001, elapsed 0.4s, est remaining 2.1s, peak mem 207MB, user 0.7s, sys 9.7s, output queue size 24
progress 20% @chr3:180000001, elapsed 0.5s, est remaining 2.1s, peak mem 222MB, user 0.9s, sys 14.2s, output queue size 6
progress 25% @chr4:107000001, elapsed 0.7s, est remaining 2.0s, peak mem 234MB, user 1.2s, sys 18.6s, output queue size 18
progress 30% @chr5:110000001, elapsed 0.8s, est remaining 1.9s, peak mem 243MB, user 1.5s, sys 23.1s, output queue size 11
progress 35% @chr6:91000001, elapsed 1.0s, est remaining 1.8s, peak mem 246MB, user 1.7s, sys 27.5s, output queue size 6
progress 40% @chr7:51000001, elapsed 1.1s, est remaining 1.7s, peak mem 252MB, user 2.1s, sys 31.8s, output queue size 26
progress 45% @chr8:49000001, elapsed 1.3s, est remaining 1.6s, peak mem 252MB, user 2.4s, sys 36.3s, output queue size 9
progress 50% @chr9:99000001, elapsed 1.4s, est remaining 1.4s, peak mem 258MB, user 2.6s, sys 40.9s, output queue size 8
progress 55% @chr10:88000001, elapsed 1.6s, est remaining 1.3s, peak mem 261MB, user 2.9s, sys 45.4s, output queue size 24
progress 60% @chr12:12000001, elapsed 1.7s, est remaining 1.2s, peak mem 261MB, user 3.2s, sys 49.9s, output queue size 8
progress 65% @chr13:1000001, elapsed 1.9s, est remaining 1.0s, peak mem 267MB, user 3.6s, sys 55.3s, output queue size 38
progress 70% @chr14:48000001, elapsed 2.2s, est remaining 0.9s, peak mem 267MB, user 3.9s, sys 62.0s, output queue size 26
progress 75% @chr16:36000001, elapsed 2.4s, est remaining 0.8s, peak mem 267MB, user 4.2s, sys 68.5s, output queue size 30
progress 80% @chr17:72000001, elapsed 2.6s, est remaining 0.7s, peak mem 267MB, user 4.6s, sys 74.9s, output queue size 25
progress 85% @chr20:11000001, elapsed 2.8s, est remaining 0.5s, peak mem 270MB, user 4.9s, sys 81.3s, output queue size 12
progress 90% @chrX:28000001, elapsed 3.2s, est remaining 0.4s, peak mem 501MB, user 7.8s, sys 85.8s, output queue size 114
progress 95% @chrY:23000001, elapsed 3.4s, est remaining 0.2s, peak mem 510MB, user 11.0s, sys 91.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.6s, est remaining 0.0s, peak mem 528MB, user 14.6s, sys 98.1s, 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: 50411664
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.012 user 0.044 sys 0.069 real
MateInfoByVcf::load: 25531 calls 4.268 user 1.100 sys 4.266 real
MateInfoByVcf::parse_events: 25531 calls 4.198 user 0.962 sys 3.960 real
advance: 3219322 calls 1.149 user 12.470 sys 13.249 real
calc: 3219322 calls 4.748 user 36.135 sys 41.302 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 0.001 user 0.005 sys 4.609 real
fetch: 3219322 calls 0.323 user 12.822 sys 11.326 real
find_pairEnds: 25531 calls 0.229 user 0.076 sys 0.399 real
idle: 1052 calls 0.044 user 0.136 sys 58.251 real
init: 1 calls 0.000 user 0.007 sys 0.006 real
markDup: 25531 calls 0.947 user 0.273 sys 1.571 real
vcfadvance: 25531 calls 0.023 user 0.182 sys 0.083 real
write: 3219322 calls 2.379 user 11.236 sys 14.885 real
overall: 553803776 mem 15.082 user 99.341 sys 5.632 real