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/3e/2dcfec0637127d92d588333474f176/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/7bc72808d1cf298ffbdcdc18ca97d8/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/34/7bc72808d1cf298ffbdcdc18ca97d8/.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/3e/2dcfec0637127d92d588333474f176/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% @chr1:141000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.2s, sys 1.5s, output queue size 20
progress 10% @chr2:71000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 2.9s, output queue size 2
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.5s, sys 4.6s, output queue size 30
progress 20% @chr3:124000001, elapsed 0.2s, est remaining 0.9s, peak mem 81MB, user 0.7s, sys 6.3s, output queue size 29
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 7.9s, output queue size 16
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 9.6s, output queue size 20
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.1s, sys 11.2s, output queue size 9
progress 40% @chr7:55000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 12.8s, output queue size 12
progress 45% @chr8:58000001, elapsed 0.5s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 14.4s, output queue size 6
progress 50% @chr9:74000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.5s, sys 16.1s, output queue size 9
progress 55% @chr10:95000001, elapsed 0.6s, est remaining 0.5s, peak mem 81MB, user 1.6s, sys 17.7s, output queue size 4
progress 60% @chr11:123000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.7s, sys 19.4s, output queue size 5
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.8s, sys 21.0s, output queue size 2
progress 70% @chr14:60000001, elapsed 0.8s, est remaining 0.3s, peak mem 81MB, user 2.0s, sys 22.6s, output queue size 1
progress 75% @chr16:12000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.2s, sys 24.2s, output queue size 1
progress 80% @chr17:82000001, elapsed 0.9s, est remaining 0.2s, peak mem 81MB, user 2.4s, sys 25.8s, output queue size 3
progress 85% @chr20:22000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.6s, sys 27.4s, output queue size 10
progress 90% @chrX:31000001, elapsed 1.1s, est remaining 0.1s, peak mem 114MB, user 3.1s, sys 28.7s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.1s, est remaining 0.1s, peak mem 141MB, user 3.5s, sys 30.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 176MB, user 4.3s, sys 33.0s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 50411666
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.024 user 0.015 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.472 user 6.746 sys 8.101 real
calc: 3219322 calls 0.416 user 5.175 sys 6.052 real
done: 1 calls 0.024 user 0.015 sys 0.048 real
execute: 1 calls 0.001 user 0.001 sys 1.395 real
fetch: 3219322 calls 0.350 user 5.130 sys 5.955 real
idle: 84 calls 0.011 user 0.016 sys 36.475 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 229548032 mem 4.495 user 33.425 sys 2.459 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% @chr1:158000001, elapsed 0.3s, est remaining 6.6s, peak mem 168MB, user 0.5s, sys 9.1s, output queue size 8
progress 10% @chr2:70000001, elapsed 0.6s, est remaining 5.8s, peak mem 177MB, user 1.0s, sys 17.6s, output queue size 29
progress 15% @chr2:226000001, elapsed 0.9s, est remaining 5.3s, peak mem 198MB, user 1.5s, sys 26.4s, output queue size 9
progress 20% @chr3:163000001, elapsed 1.2s, est remaining 4.9s, peak mem 213MB, user 1.8s, sys 34.6s, output queue size 9
progress 25% @chr4:104000001, elapsed 1.5s, est remaining 4.5s, peak mem 222MB, user 2.2s, sys 42.8s, output queue size 11
progress 30% @chr5:83000001, elapsed 1.8s, est remaining 4.1s, peak mem 225MB, user 2.6s, sys 50.9s, output queue size 3
progress 35% @chr6:67000001, elapsed 2.0s, est remaining 3.8s, peak mem 231MB, user 2.9s, sys 58.8s, output queue size 7
progress 40% @chr7:59000001, elapsed 2.3s, est remaining 3.5s, peak mem 234MB, user 3.3s, sys 67.2s, output queue size 13
progress 45% @chr8:55000001, elapsed 2.6s, est remaining 3.2s, peak mem 234MB, user 3.6s, sys 75.5s, output queue size 7
progress 50% @chr9:76000001, elapsed 2.9s, est remaining 2.9s, peak mem 240MB, user 4.0s, sys 83.7s, output queue size 14
progress 55% @chr10:100000001, elapsed 3.1s, est remaining 2.6s, peak mem 240MB, user 4.5s, sys 92.0s, output queue size 10
progress 60% @chr11:121000001, elapsed 3.4s, est remaining 2.3s, peak mem 243MB, user 4.8s, sys 100.3s, output queue size 20
progress 65% @chr13:11000001, elapsed 3.7s, est remaining 2.0s, peak mem 243MB, user 5.2s, sys 108.7s, output queue size 4
progress 70% @chr14:57000001, elapsed 4.0s, est remaining 1.7s, peak mem 246MB, user 5.5s, sys 117.0s, output queue size 4
progress 75% @chr16:18000001, elapsed 4.3s, est remaining 1.4s, peak mem 246MB, user 5.9s, sys 125.1s, output queue size 6
progress 80% @chr17:78000001, elapsed 4.5s, est remaining 1.1s, peak mem 246MB, user 6.1s, sys 133.2s, output queue size 6
progress 85% @chr20:20000001, elapsed 4.8s, est remaining 0.8s, peak mem 249MB, user 6.4s, sys 141.4s, output queue size 6
progress 90% @chrX:33000001, elapsed 5.2s, est remaining 0.6s, peak mem 498MB, user 9.3s, sys 147.6s, output queue size 114
progress 95% @chrY:34000001, elapsed 5.5s, est remaining 0.3s, peak mem 504MB, user 12.6s, sys 154.6s, output queue size 271
progress 100% @chr21:41000001, elapsed 6.5s, est remaining 0.0s, peak mem 513MB, user 16.3s, sys 163.5s, 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 6.12.83
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 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 50411666
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.007 user 0.030 sys 0.089 real
MateInfoByVcf::load: 25531 calls 3.962 user 1.703 sys 4.694 real
MateInfoByVcf::parse_events: 25531 calls 3.876 user 1.561 sys 4.302 real
advance: 3219322 calls 1.472 user 20.755 sys 22.658 real
calc: 3219322 calls 5.613 user 60.275 sys 65.879 real
done: 1 calls 0.000 user 0.000 sys 0.005 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.001 user 0.001 sys 6.590 real
fetch: 3219322 calls 0.459 user 19.681 sys 20.250 real
find_pairEnds: 25531 calls 0.209 user 0.050 sys 0.421 real
idle: 956 calls 0.045 user 0.146 sys 52.169 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
markDup: 25531 calls 0.985 user 0.277 sys 1.706 real
vcfadvance: 25531 calls 0.017 user 0.146 sys 0.125 real
write: 3219322 calls 2.996 user 20.289 sys 22.899 real
overall: 538025984 mem 16.971 user 164.603 sys 7.613 real