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/e2/c15498abb1113821317b85f5c4a1a6/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/96/affe90ad272751a557cfb55ea8a87a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e2/c15498abb1113821317b85f5c4a1a6/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% @chr1:155000001, elapsed 0.1s, est remaining 2.5s, peak mem 81MB, user 0.2s, sys 3.2s, output queue size 22
progress 10% @chr2:61000001, elapsed 0.2s, est remaining 2.2s, peak mem 81MB, user 0.3s, sys 6.6s, output queue size 18
progress 15% @chr2:231000001, elapsed 0.4s, est remaining 2.0s, peak mem 81MB, user 0.6s, sys 9.8s, output queue size 43
progress 20% @chr3:153000001, elapsed 0.5s, est remaining 1.9s, peak mem 81MB, user 0.8s, sys 13.1s, output queue size 37
progress 25% @chr4:108000001, elapsed 0.6s, est remaining 1.7s, peak mem 81MB, user 1.0s, sys 16.4s, output queue size 7
progress 30% @chr5:111000001, elapsed 0.7s, est remaining 1.6s, peak mem 81MB, user 1.1s, sys 19.7s, output queue size 22
progress 35% @chr6:62000001, elapsed 0.8s, est remaining 1.5s, peak mem 81MB, user 1.3s, sys 23.0s, output queue size 15
progress 40% @chr7:48000001, elapsed 0.9s, est remaining 1.4s, peak mem 81MB, user 1.4s, sys 26.4s, output queue size 29
progress 45% @chr8:83000001, elapsed 1.0s, est remaining 1.3s, peak mem 81MB, user 1.7s, sys 29.7s, output queue size 26
progress 50% @chr9:98000001, elapsed 1.2s, est remaining 1.2s, peak mem 81MB, user 1.9s, sys 33.1s, output queue size 21
progress 55% @chr10:88000001, elapsed 1.3s, est remaining 1.0s, peak mem 81MB, user 2.2s, sys 36.5s, output queue size 19
progress 60% @chr11:123000001, elapsed 1.4s, est remaining 0.9s, peak mem 81MB, user 2.3s, sys 40.0s, output queue size 17
progress 65% @chr13:11000001, elapsed 1.5s, est remaining 0.8s, peak mem 81MB, user 2.5s, sys 43.5s, output queue size 17
progress 70% @chr14:86000001, elapsed 1.6s, est remaining 0.7s, peak mem 81MB, user 2.7s, sys 47.0s, output queue size 22
progress 75% @chr15:92000001, elapsed 1.7s, est remaining 0.6s, peak mem 81MB, user 2.9s, sys 50.3s, output queue size 23
progress 80% @chr17:66000001, elapsed 1.9s, est remaining 0.5s, peak mem 81MB, user 3.2s, sys 54.3s, output queue size 33
progress 85% @chr20:40000001, elapsed 2.0s, est remaining 0.4s, peak mem 81MB, user 3.3s, sys 59.0s, output queue size 20
progress 90% @chrX:29000001, elapsed 2.2s, est remaining 0.2s, peak mem 93MB, user 3.9s, sys 62.8s, output queue size 114
progress 95% @chrY:23000001, elapsed 2.4s, est remaining 0.1s, peak mem 144MB, user 4.4s, sys 68.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.7s, est remaining 0.0s, peak mem 174MB, user 5.2s, sys 75.4s, 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: 49784678
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.023 user 0.015 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.253 user 15.651 sys 16.886 real
calc: 3219322 calls 0.280 user 11.913 sys 12.079 real
done: 1 calls 0.023 user 0.015 sys 0.047 real
execute: 1 calls 0.002 user 0.002 sys 2.745 real
fetch: 3219322 calls 0.328 user 12.110 sys 12.077 real
idle: 79 calls 0.002 user 0.014 sys 34.781 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 221245440 mem 5.324 user 75.823 sys 3.806 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% @chr1:160000001, elapsed 0.1s, est remaining 2.1s, peak mem 171MB, user 0.3s, sys 2.4s, output queue size 36
progress 10% @chr2:71000001, elapsed 0.2s, est remaining 1.7s, peak mem 195MB, user 0.6s, sys 4.7s, output queue size 31
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 219MB, user 0.8s, sys 7.1s, output queue size 25
progress 20% @chr3:153000001, elapsed 0.4s, est remaining 1.4s, peak mem 228MB, user 1.0s, sys 9.5s, output queue size 19
progress 25% @chr4:95000001, elapsed 0.5s, est remaining 1.4s, peak mem 231MB, user 1.2s, sys 12.4s, output queue size 20
progress 30% @chr5:81000001, elapsed 0.6s, est remaining 1.5s, peak mem 237MB, user 1.5s, sys 17.1s, output queue size 30
progress 35% @chr6:68000001, elapsed 0.8s, est remaining 1.5s, peak mem 243MB, user 1.8s, sys 21.9s, output queue size 14
progress 40% @chr7:54000001, elapsed 1.0s, est remaining 1.4s, peak mem 243MB, user 2.2s, sys 26.7s, output queue size 23
progress 45% @chr8:39000001, elapsed 1.2s, est remaining 1.4s, peak mem 252MB, user 2.5s, sys 32.0s, output queue size 18
progress 50% @chr9:62000001, elapsed 1.4s, est remaining 1.4s, peak mem 255MB, user 2.7s, sys 38.6s, output queue size 32
progress 55% @chr10:113000001, elapsed 1.6s, est remaining 1.3s, peak mem 261MB, user 3.1s, sys 45.0s, output queue size 17
progress 60% @chr11:133000001, elapsed 1.8s, est remaining 1.2s, peak mem 261MB, user 3.3s, sys 51.6s, output queue size 23
progress 65% @chr13:27000001, elapsed 2.0s, est remaining 1.1s, peak mem 264MB, user 3.6s, sys 58.4s, output queue size 21
progress 70% @chr14:67000001, elapsed 2.3s, est remaining 1.0s, peak mem 264MB, user 3.9s, sys 65.6s, output queue size 11
progress 75% @chr16:7000001, elapsed 2.5s, est remaining 0.8s, peak mem 264MB, user 4.1s, sys 72.9s, output queue size 18
progress 80% @chr18:2000001, elapsed 2.8s, est remaining 0.7s, peak mem 264MB, user 4.4s, sys 80.2s, output queue size 18
progress 85% @chr20:22000001, elapsed 3.0s, est remaining 0.5s, peak mem 267MB, user 4.7s, sys 87.4s, output queue size 1
progress 90% @chrX:28000001, elapsed 3.4s, est remaining 0.4s, peak mem 486MB, user 8.0s, sys 92.5s, output queue size 114
progress 95% @chrY:33000001, elapsed 3.6s, est remaining 0.2s, peak mem 507MB, user 10.1s, sys 98.4s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.6s, est remaining 0.0s, peak mem 519MB, user 14.2s, sys 104.7s, 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 6.12.88
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: 49784678
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.008 user 0.019 sys 0.067 real
MateInfoByVcf::load: 23378 calls 4.046 user 1.338 sys 4.097 real
MateInfoByVcf::parse_events: 23378 calls 3.976 user 1.243 sys 3.791 real
advance: 3219322 calls 1.193 user 13.242 sys 15.048 real
calc: 3219322 calls 4.663 user 39.183 sys 44.052 real
done: 1 calls 0.000 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.003 user 0.003 sys 4.676 real
fetch: 3219322 calls 0.451 user 12.440 sys 12.637 real
find_pairEnds: 23378 calls 0.203 user 0.040 sys 0.389 real
idle: 956 calls 0.023 user 0.071 sys 53.023 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.830 user 0.274 sys 1.648 real
vcfadvance: 23378 calls 0.041 user 0.096 sys 0.159 real
write: 3219322 calls 2.624 user 12.964 sys 15.544 real
overall: 544317440 mem 14.691 user 106.011 sys 5.693 real