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/8c/08acfdf6e9add2e88b07030d1ae3e6/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/960b6b37757bbf02503e473d7d51f3/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7c/960b6b37757bbf02503e473d7d51f3/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/08acfdf6e9add2e88b07030d1ae3e6/HCC1395_tumor.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 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info HCC1395_tumor.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.1s, est remaining 2.8s, peak mem 81MB, user 0.2s, sys 3.8s, output queue size 1
progress 10% @chr2:72000001, elapsed 0.3s, est remaining 2.6s, peak mem 81MB, user 0.3s, sys 7.9s, output queue size 1
progress 15% @chr2:230000001, elapsed 0.4s, est remaining 2.4s, peak mem 81MB, user 0.4s, sys 11.9s, output queue size 5
progress 20% @chr3:149000001, elapsed 0.6s, est remaining 2.2s, peak mem 81MB, user 0.6s, sys 16.1s, output queue size 4
progress 25% @chr4:115000001, elapsed 0.7s, est remaining 2.1s, peak mem 81MB, user 0.6s, sys 20.4s, output queue size 2
progress 30% @chr5:82000001, elapsed 0.8s, est remaining 2.0s, peak mem 81MB, user 0.8s, sys 24.4s, output queue size 4
progress 35% @chr6:66000001, elapsed 1.0s, est remaining 1.8s, peak mem 81MB, user 0.9s, sys 28.4s, output queue size 2
progress 40% @chr7:58000001, elapsed 1.1s, est remaining 1.7s, peak mem 81MB, user 1.1s, sys 32.5s, output queue size 2
progress 45% @chr8:60000001, elapsed 1.2s, est remaining 1.5s, peak mem 81MB, user 1.2s, sys 36.4s, output queue size 3
progress 50% @chr9:70000001, elapsed 1.4s, est remaining 1.4s, peak mem 81MB, user 1.4s, sys 40.3s, output queue size 3
progress 55% @chr10:95000001, elapsed 1.5s, est remaining 1.2s, peak mem 81MB, user 1.5s, sys 43.9s, output queue size 2
progress 60% @chr11:121000001, elapsed 1.6s, est remaining 1.1s, peak mem 81MB, user 1.7s, sys 47.3s, output queue size 5
progress 65% @chr13:8000001, elapsed 1.7s, est remaining 0.9s, peak mem 81MB, user 1.7s, sys 50.7s, output queue size 7
progress 70% @chr14:59000001, elapsed 1.8s, est remaining 0.8s, peak mem 81MB, user 1.9s, sys 54.1s, output queue size 3
progress 75% @chr16:8000001, elapsed 1.9s, est remaining 0.6s, peak mem 81MB, user 2.0s, sys 57.2s, output queue size 5
progress 80% @chr17:82000001, elapsed 2.0s, est remaining 0.5s, peak mem 81MB, user 2.1s, sys 60.3s, output queue size 2
progress 85% @chr20:16000001, elapsed 2.1s, est remaining 0.4s, peak mem 81MB, user 2.2s, sys 63.4s, output queue size 6
progress 90% @chrX:29000001, elapsed 2.3s, est remaining 0.3s, peak mem 120MB, user 2.8s, sys 65.9s, output queue size 114
progress 95% @chrY:29000001, elapsed 2.4s, est remaining 0.1s, peak mem 151MB, user 3.2s, sys 69.1s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.7s, est remaining 0.0s, peak mem 189MB, user 3.9s, sys 73.0s, 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 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.015 user 0.025 sys 0.045 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.340 user 14.082 sys 15.531 real
calc: 3219322 calls 0.440 user 11.974 sys 12.452 real
done: 1 calls 0.015 user 0.025 sys 0.045 real
execute: 1 calls 0.001 user 0.001 sys 2.655 real
fetch: 3219322 calls 0.385 user 10.816 sys 12.351 real
idle: 74 calls 0.003 user 0.017 sys 35.542 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 232071168 mem 4.030 user 73.613 sys 3.717 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i HCC1395_tumor.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info HCC1395_tumor.md.score --metrics HCC1395_tumor.md.metrics HCC1395_tumor.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:163000001, elapsed 0.1s, est remaining 2.1s, peak mem 192MB, user 0.2s, sys 2.8s, output queue size 17
progress 10% @chr2:72000001, elapsed 0.2s, est remaining 1.8s, peak mem 217MB, user 0.5s, sys 5.2s, output queue size 32
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.6s, peak mem 231MB, user 0.6s, sys 7.6s, output queue size 23
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.5s, peak mem 241MB, user 0.9s, sys 9.9s, output queue size 4
progress 25% @chr4:110000001, elapsed 0.5s, est remaining 1.4s, peak mem 252MB, user 1.0s, sys 12.5s, output queue size 17
progress 30% @chr5:86000001, elapsed 0.5s, est remaining 1.3s, peak mem 256MB, user 1.1s, sys 15.2s, output queue size 3
progress 35% @chr6:67000001, elapsed 0.6s, est remaining 1.2s, peak mem 265MB, user 1.4s, sys 17.7s, output queue size 18
progress 40% @chr7:55000001, elapsed 0.7s, est remaining 1.1s, peak mem 271MB, user 1.6s, sys 20.2s, output queue size 1
progress 45% @chr8:58000001, elapsed 0.8s, est remaining 1.0s, peak mem 276MB, user 1.7s, sys 22.8s, output queue size 12
progress 50% @chr9:73000001, elapsed 0.9s, est remaining 0.9s, peak mem 280MB, user 1.9s, sys 25.3s, output queue size 19
progress 55% @chr10:95000001, elapsed 1.0s, est remaining 0.8s, peak mem 283MB, user 2.0s, sys 27.8s, output queue size 4
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.7s, peak mem 288MB, user 2.2s, sys 30.3s, output queue size 14
progress 65% @chr13:14000001, elapsed 1.2s, est remaining 0.6s, peak mem 291MB, user 2.4s, sys 32.8s, output queue size 1
progress 70% @chr14:63000001, elapsed 1.2s, est remaining 0.5s, peak mem 297MB, user 2.5s, sys 35.3s, output queue size 6
progress 75% @chr16:15000001, elapsed 1.3s, est remaining 0.4s, peak mem 297MB, user 2.8s, sys 37.8s, output queue size 14
progress 80% @chr18:1, elapsed 1.4s, est remaining 0.4s, peak mem 297MB, user 2.9s, sys 40.3s, output queue size 6
progress 85% @chr20:20000001, elapsed 1.5s, est remaining 0.3s, peak mem 304MB, user 3.1s, sys 43.0s, output queue size 2
progress 90% @chrX:36000001, elapsed 1.7s, est remaining 0.2s, peak mem 525MB, user 5.0s, sys 44.6s, output queue size 114
progress 95% @chrY:35000001, elapsed 1.8s, est remaining 0.1s, peak mem 546MB, user 6.9s, sys 46.3s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.8s, est remaining 0.0s, peak mem 571MB, user 11.6s, sys 48.5s, output queue size 3664
library HCC1395_tumor:
chimeric_paired 1295
duped 169120
duped_chimeric_paired 30
duped_paired 169118
duped_unpaired 2
optical_dup 5868
paired 999972
reads 1001320
secondary_supplementary 1340
unmapped 4
unpaired 4
optical dup clusters 5659, maxdup 4, total optical dup pairs 5868
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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 49784676
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.010 user 0.032 sys 0.025 real
MateInfoByVcf::load: 23378 calls 3.613 user 0.794 sys 3.563 real
MateInfoByVcf::parse_events: 23378 calls 3.560 user 0.711 sys 3.445 real
advance: 3219322 calls 1.042 user 6.238 sys 7.607 real
calc: 3219322 calls 4.201 user 17.976 sys 22.282 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 0.002 user 0.002 sys 2.836 real
fetch: 3219322 calls 0.364 user 5.447 sys 6.128 real
find_pairEnds: 23378 calls 0.196 user 0.024 sys 0.336 real
idle: 2059 calls 0.232 user 0.199 sys 55.186 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.860 user 0.067 sys 1.320 real
vcfadvance: 23378 calls 0.003 user 0.045 sys 0.033 real
write: 3219322 calls 2.319 user 6.079 sys 8.200 real
overall: 599490560 mem 12.625 user 49.744 sys 3.857 real