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/70/216d116078b3706e78182344544d9a/HCC1395_tumor.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/89be7b55dd3a63d13301e5582027c4/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/89be7b55dd3a63d13301e5582027c4/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/216d116078b3706e78182344544d9a/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% @chr1:141000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 20
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 1.1s, peak mem 81MB, user 0.3s, sys 3.2s, output queue size 17
progress 15% @chr2:237000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.4s, sys 4.8s, output queue size 8
progress 20% @chr3:154000001, elapsed 0.2s, est remaining 1.0s, peak mem 81MB, user 0.5s, sys 6.4s, output queue size 23
progress 25% @chr4:118000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.6s, sys 8.3s, output queue size 10
progress 30% @chr5:87000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.8s, sys 9.9s, output queue size 2
progress 35% @chr6:66000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 0.9s, sys 11.6s, output queue size 13
progress 40% @chr7:56000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.0s, sys 13.3s, output queue size 6
progress 45% @chr8:58000001, elapsed 0.5s, est remaining 0.7s, peak mem 81MB, user 1.1s, sys 15.1s, output queue size 3
progress 50% @chr9:75000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.2s, sys 16.8s, output queue size 8
progress 55% @chr10:97000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.3s, sys 18.5s, output queue size 7
progress 60% @chr11:123000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.4s, sys 20.1s, output queue size 25
progress 65% @chr13:19000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.6s, sys 21.9s, output queue size 18
progress 70% @chr14:63000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.7s, sys 23.5s, output queue size 25
progress 75% @chr16:14000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 1.9s, sys 25.1s, output queue size 22
progress 80% @chr18:2000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.1s, sys 26.9s, output queue size 21
progress 85% @chr20:22000001, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 28.5s, output queue size 21
progress 90% @chrX:32000001, elapsed 1.1s, est remaining 0.1s, peak mem 108MB, user 2.7s, sys 30.2s, output queue size 114
progress 95% @chrY:29000001, elapsed 1.2s, est remaining 0.1s, peak mem 144MB, user 3.0s, sys 32.6s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.4s, est remaining 0.0s, peak mem 174MB, user 3.7s, sys 35.3s, 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: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.025 user 0.014 sys 0.048 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.235 user 7.399 sys 8.460 real
calc: 3219322 calls 0.284 user 5.424 sys 5.856 real
done: 1 calls 0.025 user 0.014 sys 0.048 real
execute: 1 calls 0.004 user 0.004 sys 1.417 real
fetch: 3219322 calls 0.253 user 5.535 sys 5.850 real
idle: 71 calls 0.006 user 0.022 sys 35.299 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 219021312 mem 3.834 user 35.720 sys 2.479 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 0.4s, sys 2.5s, output queue size 5
progress 10% @chr2:74000001, elapsed 0.2s, est remaining 1.8s, peak mem 192MB, user 0.8s, sys 4.6s, output queue size 9
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.6s, peak mem 213MB, user 1.0s, sys 7.0s, output queue size 16
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.5s, peak mem 222MB, user 1.5s, sys 9.1s, output queue size 18
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.3s, peak mem 228MB, user 1.8s, sys 11.4s, output queue size 6
progress 30% @chr5:88000001, elapsed 0.5s, est remaining 1.2s, peak mem 240MB, user 2.1s, sys 13.6s, output queue size 12
progress 35% @chr6:66000001, elapsed 0.6s, est remaining 1.1s, peak mem 243MB, user 2.4s, sys 16.0s, output queue size 17
progress 40% @chr7:80000001, elapsed 0.8s, est remaining 1.2s, peak mem 246MB, user 2.7s, sys 20.6s, output queue size 18
progress 45% @chr8:53000001, elapsed 0.9s, est remaining 1.2s, peak mem 249MB, user 2.9s, sys 25.3s, output queue size 19
progress 50% @chr9:68000001, elapsed 1.1s, est remaining 1.1s, peak mem 252MB, user 3.4s, sys 29.9s, output queue size 7
progress 55% @chr10:92000001, elapsed 1.3s, est remaining 1.0s, peak mem 252MB, user 3.6s, sys 34.6s, output queue size 18
progress 60% @chr12:9000001, elapsed 1.4s, est remaining 1.0s, peak mem 252MB, user 4.0s, sys 39.1s, output queue size 29
progress 65% @chr13:6000001, elapsed 1.6s, est remaining 0.9s, peak mem 252MB, user 4.3s, sys 45.5s, output queue size 28
progress 70% @chr14:50000001, elapsed 1.9s, est remaining 0.8s, peak mem 261MB, user 4.5s, sys 51.9s, output queue size 34
progress 75% @chr16:3000001, elapsed 2.1s, est remaining 0.7s, peak mem 261MB, user 4.7s, sys 58.4s, output queue size 11
progress 80% @chr17:74000001, elapsed 2.3s, est remaining 0.6s, peak mem 261MB, user 5.0s, sys 65.0s, output queue size 41
progress 85% @chr20:22000001, elapsed 2.5s, est remaining 0.4s, peak mem 264MB, user 5.2s, sys 71.6s, output queue size 11
progress 90% @chr21:13000001, elapsed 2.8s, est remaining 0.3s, peak mem 495MB, user 7.8s, sys 75.4s, output queue size 114
progress 95% @chrY:29000001, elapsed 3.1s, est remaining 0.2s, peak mem 531MB, user 10.2s, sys 81.5s, output queue size 271
progress 100% @chr21:41000001, elapsed 4.1s, est remaining 0.0s, peak mem 546MB, user 14.2s, sys 88.0s, 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: 49784677
reads: 1001320
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 23378 calls 0.008 user 0.045 sys 0.054 real
MateInfoByVcf::load: 23378 calls 3.655 user 0.886 sys 3.780 real
MateInfoByVcf::parse_events: 23378 calls 3.596 user 0.775 sys 3.530 real
advance: 3219322 calls 1.073 user 10.918 sys 12.557 real
calc: 3219322 calls 4.647 user 32.683 sys 37.692 real
done: 1 calls 0.000 user 0.001 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.002 sys 4.155 real
fetch: 3219322 calls 0.464 user 10.657 sys 10.312 real
find_pairEnds: 23378 calls 0.211 user 0.053 sys 0.374 real
idle: 998 calls 0.038 user 0.171 sys 54.778 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 23378 calls 0.828 user 0.279 sys 1.561 real
vcfadvance: 23378 calls 0.016 user 0.071 sys 0.138 real
write: 3219322 calls 2.453 user 11.017 sys 13.208 real
overall: 572628992 mem 14.703 user 88.978 sys 5.182 real