Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/d0f640285062144bf3fcc81a334178/HCC1395_BL.bam
  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/b3/57a16f0cfbc17f3f3dcbee22c14121/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/57a16f0cfbc17f3f3dcbee22c14121/.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/55/d0f640285062144bf3fcc81a334178/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% @chr1:173000001, elapsed 0.1s, est remaining 1.4s, peak mem 81MB, user 0.2s, sys 1.6s, output queue size 14
progress 10% @chr2:80000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.5s, sys 3.3s, output queue size 18
progress 15% @chr2:220000001, elapsed 0.2s, est remaining 1.2s, peak mem 81MB, user 0.8s, sys 5.1s, output queue size 16
progress 20% @chr3:158000001, elapsed 0.3s, est remaining 1.1s, peak mem 81MB, user 1.0s, sys 6.8s, output queue size 16
progress 25% @chr4:122000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 1.3s, sys 8.5s, output queue size 19
progress 30% @chr5:68000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 1.5s, sys 10.3s, output queue size 18
progress 35% @chr6:68000001, elapsed 0.5s, est remaining 0.9s, peak mem 81MB, user 1.7s, sys 12.1s, output queue size 12
progress 40% @chr7:63000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 2.0s, sys 13.8s, output queue size 12
progress 45% @chr8:63000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 2.3s, sys 15.5s, output queue size 19
progress 50% @chr9:78000001, elapsed 0.7s, est remaining 0.7s, peak mem 81MB, user 2.5s, sys 17.3s, output queue size 10
progress 55% @chr10:99000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 2.7s, sys 19.1s, output queue size 14
progress 60% @chr11:131000001, elapsed 0.8s, est remaining 0.5s, peak mem 81MB, user 2.9s, sys 20.9s, output queue size 17
progress 65% @chr13:22000001, elapsed 0.9s, est remaining 0.5s, peak mem 81MB, user 3.2s, sys 22.6s, output queue size 15
progress 70% @chr14:41000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 3.4s, sys 24.4s, output queue size 20
progress 75% @chr16:20000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 3.6s, sys 26.2s, output queue size 17
progress 80% @chr17:62000001, elapsed 1.0s, est remaining 0.3s, peak mem 81MB, user 3.8s, sys 28.0s, output queue size 22
progress 85% @chr20:28000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 4.1s, sys 29.7s, output queue size 17
progress 90% @chrX:34000001, elapsed 1.2s, est remaining 0.1s, peak mem 121MB, user 4.7s, sys 31.1s, output queue size 114
progress 95% @chrY:18000001, elapsed 1.3s, est remaining 0.1s, peak mem 150MB, user 5.2s, sys 33.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.6s, est remaining 0.0s, peak mem 193MB, user 5.9s, sys 35.7s, 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: 50406994
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.025 user 0.015 sys 0.047 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.245 user 6.505 sys 8.908 real
calc: 3219322 calls 0.385 user 4.975 sys 6.511 real
done: 1 calls 0.025 user 0.015 sys 0.047 real
execute: 1 calls 0.001 user 0.002 sys 1.552 real
fetch: 3219322 calls 0.425 user 5.329 sys 6.467 real
idle: 75 calls 0.008 user 0.026 sys 36.638 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 243314688 mem 6.106 user 36.231 sys 2.616 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% @chr1:167000001, elapsed 0.1s, est remaining 2.2s, peak mem 184MB, user 0.3s, sys 2.6s, output queue size 12
progress 10% @chr2:78000001, elapsed 0.2s, est remaining 1.8s, peak mem 216MB, user 0.6s, sys 5.0s, output queue size 14
progress 15% @chr3:1, elapsed 0.3s, est remaining 1.7s, peak mem 240MB, user 1.1s, sys 7.3s, output queue size 19
progress 20% @chr3:161000001, elapsed 0.4s, est remaining 1.5s, peak mem 246MB, user 1.5s, sys 9.5s, output queue size 22
progress 25% @chr4:120000001, elapsed 0.5s, est remaining 1.4s, peak mem 252MB, user 2.0s, sys 11.8s, output queue size 14
progress 30% @chr5:92000001, elapsed 0.6s, est remaining 1.3s, peak mem 258MB, user 2.4s, sys 14.1s, output queue size 19
progress 35% @chr6:73000001, elapsed 0.6s, est remaining 1.2s, peak mem 264MB, user 2.7s, sys 16.6s, output queue size 17
progress 40% @chr7:60000001, elapsed 0.7s, est remaining 1.1s, peak mem 271MB, user 3.0s, sys 18.9s, output queue size 33
progress 45% @chr8:61000001, elapsed 0.8s, est remaining 1.0s, peak mem 279MB, user 3.4s, sys 21.3s, output queue size 24
progress 50% @chr9:78000001, elapsed 0.9s, est remaining 0.9s, peak mem 280MB, user 3.9s, sys 23.6s, output queue size 18
progress 55% @chr10:102000001, elapsed 1.0s, est remaining 0.8s, peak mem 280MB, user 4.1s, sys 26.1s, output queue size 35
progress 60% @chr11:127000001, elapsed 1.1s, est remaining 0.7s, peak mem 282MB, user 4.5s, sys 28.5s, output queue size 40
progress 65% @chr13:17000001, elapsed 1.2s, est remaining 0.6s, peak mem 283MB, user 4.9s, sys 30.9s, output queue size 24
progress 70% @chr14:49000001, elapsed 1.3s, est remaining 0.5s, peak mem 286MB, user 5.2s, sys 33.5s, output queue size 20
progress 75% @chr16:15000001, elapsed 1.4s, est remaining 0.5s, peak mem 288MB, user 5.6s, sys 36.0s, output queue size 16
progress 80% @chr17:82000001, elapsed 1.5s, est remaining 0.4s, peak mem 288MB, user 5.8s, sys 38.8s, output queue size 2
progress 85% @chr20:23000001, elapsed 1.6s, est remaining 0.3s, peak mem 289MB, user 6.0s, sys 41.6s, output queue size 6
progress 90% @chrX:39000001, elapsed 1.7s, est remaining 0.2s, peak mem 526MB, user 7.9s, sys 43.1s, output queue size 114
progress 95% @chrY:39000001, elapsed 1.8s, est remaining 0.1s, peak mem 547MB, user 9.2s, sys 44.2s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.0s, est remaining 0.0s, peak mem 574MB, user 14.9s, sys 45.9s, 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 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 50406994
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.010 user 0.002 sys 0.023 real
MateInfoByVcf::load: 25531 calls 4.309 user 0.628 sys 3.911 real
MateInfoByVcf::parse_events: 25531 calls 4.242 user 0.604 sys 3.798 real
advance: 3219322 calls 1.153 user 5.084 sys 7.555 real
calc: 3219322 calls 4.759 user 16.795 sys 22.113 real
done: 1 calls 0.001 user 0.000 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.005 sys 0.001 real
execute: 1 calls 0.003 user 0.004 sys 3.033 real
fetch: 3219322 calls 0.433 user 5.217 sys 6.434 real
find_pairEnds: 25531 calls 0.208 user 0.021 sys 0.332 real
idle: 1891 calls 0.138 user 0.210 sys 60.482 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 25531 calls 0.725 user 0.082 sys 1.284 real
vcfadvance: 25531 calls 0.020 user 0.090 sys 0.033 real
write: 3219322 calls 2.555 user 6.034 sys 7.973 real
overall: 602710016 mem 15.762 user 46.987 sys 4.038 real