Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/5742daf5f56600562722d42cf5d023/Filler-D0001361.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/9a/c98f22ad5f7fb9296f3a3df432dc03/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9a/c98f22ad5f7fb9296f3a3df432dc03/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/5742daf5f56600562722d42cf5d023/Filler-D0001361.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 Filler-D0001361.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Filler-D0001361.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:187000001, elapsed 2.3s, est remaining 44.5s, peak mem 1400MB, user 52.5s, sys 5.1s, output queue size 160
progress 10% @chr2:89000001, elapsed 3.8s, est remaining 34.4s, peak mem 1593MB, user 104.1s, sys 6.2s, output queue size 94
progress 15% @chr3:3000001, elapsed 5.4s, est remaining 30.5s, peak mem 2431MB, user 148.1s, sys 7.1s, output queue size 203
progress 20% @chr3:150000001, elapsed 7.1s, est remaining 28.4s, peak mem 3614MB, user 188.9s, sys 7.9s, output queue size 364
progress 25% @chr4:120000001, elapsed 8.2s, est remaining 24.7s, peak mem 4610MB, user 229.8s, sys 9.0s, output queue size 525
progress 30% @chr5:97000001, elapsed 9.1s, est remaining 21.3s, peak mem 5207MB, user 259.0s, sys 9.8s, output queue size 687
progress 35% @chr6:91000001, elapsed 10.7s, est remaining 19.8s, peak mem 6302MB, user 297.5s, sys 10.3s, output queue size 848
progress 40% @chr7:79000001, elapsed 12.1s, est remaining 18.1s, peak mem 7309MB, user 334.9s, sys 11.1s, output queue size 1009
progress 45% @chr8:78000001, elapsed 13.8s, est remaining 16.9s, peak mem 8812MB, user 386.8s, sys 12.4s, output queue size 1171
progress 50% @chr9:88000001, elapsed 15.0s, est remaining 15.0s, peak mem 9695MB, user 424.5s, sys 13.3s, output queue size 1333
progress 55% @chr10:95000001, elapsed 16.9s, est remaining 13.9s, peak mem 10662MB, user 473.1s, sys 15.0s, output queue size 1494
progress 60% @chr11:61000001, elapsed 19.0s, est remaining 12.6s, peak mem 11125MB, user 534.6s, sys 16.1s, output queue size 1656
progress 65% @chr12:109000001, elapsed 20.7s, est remaining 11.2s, peak mem 11429MB, user 585.0s, sys 16.7s, output queue size 1818
progress 70% @chr13:98000001, elapsed 22.5s, est remaining 9.6s, peak mem 11654MB, user 640.0s, sys 17.5s, output queue size 1979
progress 75% @chr16:33000001, elapsed 24.6s, est remaining 8.2s, peak mem 11725MB, user 693.0s, sys 18.0s, output queue size 2141
progress 80% @chr17:74000001, elapsed 28.7s, est remaining 7.2s, peak mem 12519MB, user 794.3s, sys 19.1s, output queue size 2303
progress 85% @chr20:42000001, elapsed 32.3s, est remaining 5.7s, peak mem 12828MB, user 918.8s, sys 20.3s, output queue size 2465
progress 90% @chrX:35000001, elapsed 36.0s, est remaining 4.0s, peak mem 14438MB, user 1044.1s, sys 28.2s, output queue size 529
progress 95% @chrY:49000001, elapsed 37.4s, est remaining 2.0s, peak mem 15161MB, user 1078.4s, sys 28.8s, output queue size 691
progress 100% @chr19:7000001, elapsed 74.1s, est remaining 0.0s, peak mem 21307MB, user 1223.8s, sys 40.3s, output queue size 3822
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: 30561623826
reads: 995299818
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 4.295 user 0.915 sys 5.920 real
VcfLineRecordHelper::sort: 123 calls 6.583 user 0.399 sys 7.003 real
advance: 3219322 calls 651.987 user 30.212 sys 683.435 real
calc: 3219322 calls 265.085 user 4.352 sys 269.510 real
done: 1 calls 4.295 user 0.915 sys 5.920 real
execute: 1 calls 0.003 user 0.005 sys 74.117 real
fetch: 3219322 calls 259.292 user 2.598 sys 263.677 real
idle: 1290 calls 0.361 user 0.005 sys 1238.035 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 22345846784 mem 1248.495 user 42.575 sys 81.267 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Filler-D0001361.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Filler-D0001361.md.score --metrics Filler-D0001361.md.metrics Filler-D0001361.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:167000001, elapsed 12.8s, est remaining 243.2s, peak mem 1825MB, user 321.7s, sys 6.7s, output queue size 52
progress 10% @chr2:92000001, elapsed 21.1s, est remaining 189.7s, peak mem 2333MB, user 606.6s, sys 9.9s, output queue size 47
progress 15% @chr3:3000001, elapsed 30.1s, est remaining 170.4s, peak mem 7939MB, user 852.8s, sys 12.9s, output queue size 203
progress 20% @chr3:161000001, elapsed 39.9s, est remaining 159.4s, peak mem 12146MB, user 1131.5s, sys 16.3s, output queue size 364
progress 25% @chr4:131000001, elapsed 46.7s, est remaining 140.0s, peak mem 13110MB, user 1366.7s, sys 18.9s, output queue size 525
progress 30% @chr5:81000001, elapsed 52.6s, est remaining 122.8s, peak mem 13686MB, user 1529.0s, sys 20.7s, output queue size 687
progress 35% @chr6:72000001, elapsed 62.1s, est remaining 115.3s, peak mem 15015MB, user 1774.9s, sys 23.0s, output queue size 848
progress 40% @chr7:50000001, elapsed 70.9s, est remaining 106.4s, peak mem 15119MB, user 2046.5s, sys 26.4s, output queue size 1009
progress 45% @chr8:71000001, elapsed 81.1s, est remaining 99.1s, peak mem 15821MB, user 2351.8s, sys 29.4s, output queue size 1171
progress 50% @chr9:39000001, elapsed 88.2s, est remaining 88.2s, peak mem 17034MB, user 2543.1s, sys 31.8s, output queue size 1333
progress 55% @chr10:87000001, elapsed 100.4s, est remaining 82.1s, peak mem 17034MB, user 2888.1s, sys 34.7s, output queue size 1494
progress 60% @chr11:113000001, elapsed 114.4s, est remaining 76.3s, peak mem 17034MB, user 3265.6s, sys 38.2s, output queue size 1656
progress 65% @chr13:19000001, elapsed 125.4s, est remaining 67.5s, peak mem 17034MB, user 3594.3s, sys 40.8s, output queue size 1818
progress 70% @chr14:83000001, elapsed 136.5s, est remaining 58.5s, peak mem 17034MB, user 3945.1s, sys 43.4s, output queue size 1979
progress 75% @chr16:41000001, elapsed 148.9s, est remaining 49.6s, peak mem 17034MB, user 4260.7s, sys 45.6s, output queue size 2141
progress 80% @chr17:42000001, elapsed 172.7s, est remaining 43.2s, peak mem 17976MB, user 4983.5s, sys 49.5s, output queue size 2303
progress 85% @chr20:23000001, elapsed 195.3s, est remaining 34.5s, peak mem 17976MB, user 5614.0s, sys 53.5s, output queue size 2465
progress 90% @chrX:35000001, elapsed 220.4s, est remaining 24.5s, peak mem 22364MB, user 6289.5s, sys 57.1s, output queue size 2627
progress 95% @chrY:54000001, elapsed 229.8s, est remaining 12.1s, peak mem 22364MB, user 6532.5s, sys 58.5s, output queue size 2789
progress 100% @chr19:7000001, elapsed 364.8s, est remaining 0.0s, peak mem 26880MB, user 7427.7s, sys 79.2s, output queue size 3822
library Filler-D0001361:
chimeric_paired 30886655
duped 761295395
duped_chimeric_paired 13035206
duped_paired 761279636
duped_unpaired 15759
optical_dup 98359583
paired 986078160
reads 995287138
secondary_supplementary 9175318
unmapped 29510
unpaired 16830
optical dup clusters 37539549, maxdup 291, total optical dup pairs 98359583
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: 30561623826
reads: 995299818
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 2576915 calls 43.874 user 1.189 sys 45.855 real
MateInfoByVcf::load: 2576915 calls 1431.296 user 14.409 sys 1288.118 real
MateInfoByVcf::parse_events: 2576915 calls 1233.725 user 11.142 sys 1169.864 real
advance: 3219322 calls 598.108 user 22.499 sys 727.177 real
calc: 3219322 calls 4884.616 user 34.320 sys 5028.435 real
done: 1 calls 0.044 user 0.009 sys 0.061 real
exec_no_coor: 1 calls 0.047 user 0.045 sys 0.119 real
execute: 1 calls 0.007 user 0.001 sys 366.540 real
fetch: 3219323 calls 381.135 user 2.564 sys 354.821 real
find_pairEnds: 2576915 calls 419.546 user 1.846 sys 466.614 real
idle: 314831 calls 59.177 user 3.375 sys 3753.860 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 2576915 calls 1752.898 user 12.896 sys 1959.349 real
vcfadvance: 2576915 calls 9.078 user 2.236 sys 10.417 real
write: 3219323 calls 3089.518 user 20.281 sys 3016.134 real
overall: 28185837568 mem 7509.335 user 97.272 sys 368.865 real