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/c3/5506df0a357cd11929604eb852eb91/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/574436cf095b44b921278c1b906493/Sig_18_tissue.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/5506df0a357cd11929604eb852eb91/.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/40/574436cf095b44b921278c1b906493/Sig_18_tissue.bai
==> STAGING COMPLETE (6 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_tissue.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:161000001, elapsed 0.1s, est remaining 1.9s, peak mem 81MB, user 0.2s, sys 2.3s, output queue size 1
progress 10% @chr2:71000001, elapsed 0.2s, est remaining 1.8s, peak mem 81MB, user 0.4s, sys 5.3s, output queue size 6
progress 15% @chr2:234000001, elapsed 0.3s, est remaining 1.7s, peak mem 81MB, user 0.6s, sys 7.9s, output queue size 3
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.6s, peak mem 81MB, user 0.8s, sys 10.7s, output queue size 18
progress 25% @chr4:115000001, elapsed 0.5s, est remaining 1.5s, peak mem 81MB, user 0.9s, sys 13.8s, output queue size 1
progress 30% @chr5:84000001, elapsed 0.6s, est remaining 1.4s, peak mem 81MB, user 1.1s, sys 16.7s, output queue size 4
progress 35% @chr6:68000001, elapsed 0.7s, est remaining 1.3s, peak mem 81MB, user 1.3s, sys 19.5s, output queue size 9
progress 40% @chr7:56000001, elapsed 0.8s, est remaining 1.2s, peak mem 81MB, user 1.6s, sys 22.1s, output queue size 14
progress 45% @chr8:59000001, elapsed 0.9s, est remaining 1.1s, peak mem 81MB, user 1.8s, sys 24.8s, output queue size 6
progress 50% @chr9:75000001, elapsed 1.0s, est remaining 1.0s, peak mem 81MB, user 2.0s, sys 27.5s, output queue size 16
progress 55% @chr10:96000001, elapsed 1.1s, est remaining 0.9s, peak mem 81MB, user 2.2s, sys 30.2s, output queue size 11
progress 60% @chr11:118000001, elapsed 1.2s, est remaining 0.8s, peak mem 81MB, user 2.5s, sys 32.9s, output queue size 5
progress 65% @chr13:12000001, elapsed 1.3s, est remaining 0.7s, peak mem 81MB, user 2.7s, sys 35.7s, output queue size 3
progress 70% @chr14:44000001, elapsed 1.4s, est remaining 0.6s, peak mem 81MB, user 2.9s, sys 38.6s, output queue size 17
progress 75% @chr16:13000001, elapsed 1.5s, est remaining 0.5s, peak mem 81MB, user 3.0s, sys 41.4s, output queue size 8
progress 80% @chr17:82000001, elapsed 1.6s, est remaining 0.4s, peak mem 81MB, user 3.2s, sys 44.1s, output queue size 14
progress 85% @chr20:19000001, elapsed 1.6s, est remaining 0.3s, peak mem 81MB, user 3.4s, sys 46.8s, output queue size 10
progress 90% @chrX:26000001, elapsed 1.8s, est remaining 0.2s, peak mem 124MB, user 4.4s, sys 49.4s, output queue size 114
progress 95% @chrY:29000001, elapsed 1.9s, est remaining 0.1s, peak mem 151MB, user 4.8s, sys 52.7s, output queue size 271
progress 100% @chr21:41000001, elapsed 2.2s, est remaining 0.0s, peak mem 169MB, user 5.6s, sys 56.4s, 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: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.031 user 0.010 sys 0.043 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.787 user 10.917 sys 13.214 real
calc: 3219322 calls 0.491 user 9.092 sys 9.705 real
done: 1 calls 0.031 user 0.010 sys 0.043 real
execute: 1 calls 0.001 user 0.001 sys 2.245 real
fetch: 3219322 calls 0.435 user 8.564 sys 9.722 real
idle: 71 calls 0.001 user 0.009 sys 37.670 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 220356608 mem 5.745 user 56.963 sys 3.316 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_tissue.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_tissue.md.score --metrics Sig_18_tissue.md.metrics Sig_18_tissue.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.2s, est remaining 4.6s, peak mem 194MB, user 0.3s, sys 4.8s, output queue size 16
progress 10% @chr2:71000001, elapsed 0.4s, est remaining 4.0s, peak mem 220MB, user 0.7s, sys 10.7s, output queue size 2
progress 15% @chr2:234000001, elapsed 0.7s, est remaining 3.7s, peak mem 238MB, user 1.1s, sys 16.8s, output queue size 4
progress 20% @chr3:155000001, elapsed 0.9s, est remaining 3.4s, peak mem 251MB, user 1.4s, sys 22.6s, output queue size 20
progress 25% @chr4:115000001, elapsed 1.1s, est remaining 3.2s, peak mem 260MB, user 1.8s, sys 28.7s, output queue size 16
progress 30% @chr5:89000001, elapsed 1.3s, est remaining 3.0s, peak mem 268MB, user 2.2s, sys 34.6s, output queue size 7
progress 35% @chr6:65000001, elapsed 1.5s, est remaining 2.7s, peak mem 275MB, user 2.4s, sys 40.2s, output queue size 9
progress 40% @chr7:55000001, elapsed 1.6s, est remaining 2.5s, peak mem 278MB, user 2.8s, sys 45.8s, output queue size 2
progress 45% @chr8:63000001, elapsed 1.8s, est remaining 2.3s, peak mem 283MB, user 3.2s, sys 51.3s, output queue size 13
progress 50% @chr9:77000001, elapsed 2.0s, est remaining 2.0s, peak mem 283MB, user 3.6s, sys 56.4s, output queue size 13
progress 55% @chr10:74000001, elapsed 2.2s, est remaining 1.8s, peak mem 284MB, user 4.0s, sys 61.6s, output queue size 21
progress 60% @chr11:121000001, elapsed 2.4s, est remaining 1.6s, peak mem 287MB, user 4.3s, sys 66.8s, output queue size 14
progress 65% @chr13:24000001, elapsed 2.5s, est remaining 1.4s, peak mem 290MB, user 4.6s, sys 71.5s, output queue size 7
progress 70% @chr14:60000001, elapsed 2.7s, est remaining 1.2s, peak mem 292MB, user 5.0s, sys 76.2s, output queue size 1
progress 75% @chr16:15000001, elapsed 2.9s, est remaining 1.0s, peak mem 295MB, user 5.2s, sys 81.1s, output queue size 1
progress 80% @chr18:1, elapsed 3.1s, est remaining 0.8s, peak mem 296MB, user 5.6s, sys 86.9s, output queue size 7
progress 85% @chr20:1000001, elapsed 3.3s, est remaining 0.6s, peak mem 298MB, user 6.2s, sys 93.5s, output queue size 21
progress 90% @chrX:38000001, elapsed 3.8s, est remaining 0.4s, peak mem 517MB, user 10.2s, sys 98.4s, output queue size 114
progress 95% @chrY:32000001, elapsed 4.0s, est remaining 0.2s, peak mem 527MB, user 14.4s, sys 104.5s, output queue size 240
progress 100% @chr21:41000001, elapsed 4.7s, est remaining 0.0s, peak mem 535MB, user 17.5s, sys 111.1s, output queue size 3664
library Sig_18_tissue:
chimeric_paired 1886
duped 84376
duped_chimeric_paired 8
duped_paired 84374
duped_unpaired 2
optical_dup 3799
paired 999968
reads 1001834
secondary_supplementary 1858
unmapped 8
unpaired 4
optical dup clusters 3695, maxdup 3, total optical dup pairs 3799
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: 49121344
reads: 1001838
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 28282 calls 0.009 user 0.065 sys 0.085 real
MateInfoByVcf::load: 28282 calls 4.994 user 1.892 sys 5.714 real
MateInfoByVcf::parse_events: 28282 calls 4.932 user 1.695 sys 5.347 real
advance: 3219322 calls 1.884 user 13.690 sys 17.271 real
calc: 3219322 calls 5.380 user 40.724 sys 46.965 real
done: 1 calls 0.000 user 0.003 sys 0.004 real
exec_no_coor: 1 calls 0.000 user 0.003 sys 0.003 real
execute: 1 calls 0.009 user 0.000 sys 4.759 real
fetch: 3219323 calls 0.574 user 13.059 sys 14.301 real
find_pairEnds: 28282 calls 0.264 user 0.052 sys 0.496 real
idle: 1041 calls 0.388 user 0.346 sys 42.739 real
init: 1 calls 0.003 user 0.000 sys 0.008 real
markDup: 28282 calls 1.170 user 0.376 sys 2.214 real
vcfadvance: 28282 calls 0.040 user 0.176 sys 0.199 real
write: 3219323 calls 2.582 user 13.983 sys 16.177 real
overall: 561958912 mem 18.856 user 112.360 sys 5.775 real