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/f1/397c62f870c5f63abaa13a57e65f8d/HCC1395_BL.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/fd9523c3e5735afb5e90371124c285/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2b/fd9523c3e5735afb5e90371124c285/.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/f1/397c62f870c5f63abaa13a57e65f8d/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% @chr1:162000001, elapsed 0.1s, est remaining 2.2s, peak mem 81MB, user 0.1s, sys 2.9s, output queue size 17
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 2.0s, peak mem 81MB, user 0.3s, sys 5.9s, output queue size 1
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.8s, peak mem 81MB, user 0.5s, sys 8.9s, output queue size 16
progress 20% @chr3:150000001, elapsed 0.4s, est remaining 1.8s, peak mem 81MB, user 0.7s, sys 12.5s, output queue size 6
progress 25% @chr4:118000001, elapsed 0.6s, est remaining 1.7s, peak mem 81MB, user 0.8s, sys 16.2s, output queue size 10
progress 30% @chr5:85000001, elapsed 0.7s, est remaining 1.6s, peak mem 81MB, user 1.1s, sys 19.8s, output queue size 16
progress 35% @chr6:65000001, elapsed 0.8s, est remaining 1.5s, peak mem 81MB, user 1.3s, sys 22.9s, output queue size 2
progress 40% @chr7:58000001, elapsed 0.9s, est remaining 1.4s, peak mem 81MB, user 1.5s, sys 26.2s, output queue size 11
progress 45% @chr8:58000001, elapsed 1.0s, est remaining 1.2s, peak mem 81MB, user 1.7s, sys 29.3s, output queue size 18
progress 50% @chr9:76000001, elapsed 1.1s, est remaining 1.1s, peak mem 81MB, user 2.0s, sys 32.3s, output queue size 24
progress 55% @chr10:93000001, elapsed 1.2s, est remaining 1.0s, peak mem 81MB, user 2.2s, sys 35.2s, output queue size 2
progress 60% @chr11:124000001, elapsed 1.3s, est remaining 0.9s, peak mem 81MB, user 2.3s, sys 38.0s, output queue size 13
progress 65% @chr13:15000001, elapsed 1.4s, est remaining 0.8s, peak mem 81MB, user 2.5s, sys 40.6s, output queue size 1
progress 70% @chr14:63000001, elapsed 1.5s, est remaining 0.6s, peak mem 81MB, user 2.6s, sys 43.5s, output queue size 11
progress 75% @chr15:87000001, elapsed 1.6s, est remaining 0.5s, peak mem 81MB, user 2.8s, sys 46.4s, output queue size 28
progress 80% @chr17:56000001, elapsed 1.7s, est remaining 0.4s, peak mem 81MB, user 3.0s, sys 49.5s, output queue size 28
progress 85% @chr20:24000001, elapsed 1.8s, est remaining 0.3s, peak mem 81MB, user 3.3s, sys 52.7s, output queue size 5
progress 90% @chrX:29000001, elapsed 2.0s, est remaining 0.2s, peak mem 120MB, user 4.2s, sys 55.8s, output queue size 114
progress 95% @chrY:33000001, elapsed 2.1s, est remaining 0.1s, peak mem 147MB, user 4.7s, sys 59.3s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.5s, est remaining 0.0s, peak mem 183MB, user 5.7s, sys 63.7s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 50411659
reads: 1001089
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.018 user 0.037 sys 0.057 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.977 user 12.358 sys 14.939 real
calc: 3219322 calls 0.430 user 10.413 sys 10.887 real
done: 1 calls 0.018 user 0.037 sys 0.057 real
execute: 1 calls 0.001 user 0.003 sys 2.482 real
fetch: 3219322 calls 0.540 user 10.248 sys 10.906 real
idle: 83 calls 0.008 user 0.018 sys 37.569 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 233807872 mem 5.820 user 64.408 sys 3.555 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% @chr1:149000001, elapsed 0.2s, est remaining 2.9s, peak mem 190MB, user 0.4s, sys 3.8s, output queue size 12
progress 10% @chr2:77000001, elapsed 0.3s, est remaining 2.5s, peak mem 220MB, user 0.7s, sys 7.4s, output queue size 11
progress 15% @chr2:236000001, elapsed 0.4s, est remaining 2.3s, peak mem 247MB, user 1.0s, sys 10.9s, output queue size 20
progress 20% @chr3:156000001, elapsed 0.5s, est remaining 2.1s, peak mem 256MB, user 1.3s, sys 14.5s, output queue size 12
progress 25% @chr4:110000001, elapsed 0.7s, est remaining 2.0s, peak mem 266MB, user 1.7s, sys 18.0s, output queue size 7
progress 30% @chr5:89000001, elapsed 0.8s, est remaining 1.8s, peak mem 268MB, user 2.1s, sys 21.4s, output queue size 10
progress 35% @chr6:66000001, elapsed 0.9s, est remaining 1.7s, peak mem 272MB, user 2.5s, sys 24.8s, output queue size 18
progress 40% @chr7:56000001, elapsed 1.0s, est remaining 1.5s, peak mem 278MB, user 2.8s, sys 28.4s, output queue size 4
progress 45% @chr8:44000001, elapsed 1.2s, est remaining 1.4s, peak mem 283MB, user 3.2s, sys 32.0s, output queue size 14
progress 50% @chr9:70000001, elapsed 1.3s, est remaining 1.3s, peak mem 287MB, user 3.5s, sys 36.2s, output queue size 3
progress 55% @chr10:80000001, elapsed 1.4s, est remaining 1.2s, peak mem 287MB, user 3.7s, sys 40.0s, output queue size 15
progress 60% @chr11:121000001, elapsed 1.6s, est remaining 1.1s, peak mem 290MB, user 4.0s, sys 43.8s, output queue size 7
progress 65% @chr13:14000001, elapsed 1.7s, est remaining 0.9s, peak mem 292MB, user 4.4s, sys 47.5s, output queue size 1
progress 70% @chr14:58000001, elapsed 1.8s, est remaining 0.8s, peak mem 292MB, user 4.8s, sys 51.3s, output queue size 12
progress 75% @chr16:14000001, elapsed 2.0s, est remaining 0.7s, peak mem 295MB, user 5.1s, sys 55.1s, output queue size 5
progress 80% @chr18:4000001, elapsed 2.1s, est remaining 0.5s, peak mem 295MB, user 5.4s, sys 59.1s, output queue size 8
progress 85% @chr20:26000001, elapsed 2.3s, est remaining 0.4s, peak mem 298MB, user 5.8s, sys 63.4s, output queue size 1
progress 90% @chrX:40000001, elapsed 2.5s, est remaining 0.3s, peak mem 527MB, user 8.6s, sys 65.5s, output queue size 114
progress 95% @chrY:35000001, elapsed 2.7s, est remaining 0.1s, peak mem 547MB, user 10.4s, sys 67.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 3.5s, est remaining 0.0s, peak mem 572MB, user 17.3s, sys 70.2s, 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: 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: 50411659
reads: 1001089
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 25531 calls 0.002 user 0.002 sys 0.033 real
MateInfoByVcf::load: 25531 calls 5.670 user 0.972 sys 5.315 real
MateInfoByVcf::parse_events: 25531 calls 5.599 user 0.918 sys 5.161 real
advance: 3219322 calls 1.672 user 8.575 sys 11.077 real
calc: 3219322 calls 4.991 user 25.011 sys 31.255 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 0.009 user 0.001 sys 3.534 real
fetch: 3219322 calls 0.605 user 8.193 sys 9.333 real
find_pairEnds: 25531 calls 0.206 user 0.020 sys 0.434 real
idle: 1685 calls 0.798 user 0.283 sys 48.067 real
init: 1 calls 0.003 user 0.000 sys 0.008 real
markDup: 25531 calls 1.036 user 0.085 sys 1.794 real
vcfadvance: 25531 calls 0.011 user 0.098 sys 0.045 real
write: 3219322 calls 2.335 user 8.663 sys 10.775 real
overall: 599941120 mem 19.294 user 71.445 sys 4.560 real