cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 659_eKx-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 1.4s, peak mem 82MB, user 0.2s, sys 1.4s, output queue size 8
progress 10% @chr2:75000001, elapsed 0.1s, est remaining 1.2s, peak mem 85MB, user 0.3s, sys 3.2s, output queue size 41
progress 15% @chr2:234000001, elapsed 0.2s, est remaining 1.2s, peak mem 94MB, user 0.6s, sys 5.2s, output queue size 5
progress 20% @chr3:154000001, elapsed 0.3s, est remaining 1.1s, peak mem 94MB, user 0.7s, sys 6.9s, output queue size 15
progress 25% @chr4:115000001, elapsed 0.3s, est remaining 1.0s, peak mem 94MB, user 0.9s, sys 8.6s, output queue size 21
progress 30% @chr5:65000001, elapsed 0.4s, est remaining 0.9s, peak mem 94MB, user 1.0s, sys 10.3s, output queue size 21
progress 35% @chr6:64000001, elapsed 0.4s, est remaining 0.8s, peak mem 94MB, user 1.2s, sys 11.9s, output queue size 1
progress 40% @chr7:54000001, elapsed 0.5s, est remaining 0.8s, peak mem 94MB, user 1.4s, sys 13.6s, output queue size 1
progress 45% @chr8:56000001, elapsed 0.6s, est remaining 0.7s, peak mem 94MB, user 1.6s, sys 15.3s, output queue size 1
progress 50% @chr9:73000001, elapsed 0.6s, est remaining 0.6s, peak mem 94MB, user 1.8s, sys 16.9s, output queue size 11
progress 55% @chr10:95000001, elapsed 0.7s, est remaining 0.6s, peak mem 94MB, user 1.9s, sys 18.7s, output queue size 5
progress 60% @chr11:122000001, elapsed 0.7s, est remaining 0.5s, peak mem 94MB, user 2.1s, sys 20.3s, output queue size 5
progress 65% @chr13:14000001, elapsed 0.8s, est remaining 0.4s, peak mem 94MB, user 2.3s, sys 22.1s, output queue size 1
progress 70% @chr14:61000001, elapsed 0.9s, est remaining 0.4s, peak mem 94MB, user 2.4s, sys 23.8s, output queue size 4
progress 75% @chr16:13000001, elapsed 0.9s, est remaining 0.3s, peak mem 94MB, user 2.5s, sys 25.6s, output queue size 10
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 94MB, user 2.7s, sys 27.3s, output queue size 12
progress 85% @chr20:21000001, elapsed 1.1s, est remaining 0.2s, peak mem 94MB, user 2.9s, sys 28.9s, output queue size 72
progress 90% @chrX:20000001, elapsed 1.1s, est remaining 0.1s, peak mem 94MB, user 3.1s, sys 30.7s, output queue size 1
progress 95% @chrY:26000001, elapsed 1.2s, est remaining 0.1s, peak mem 94MB, user 3.3s, sys 32.4s, output queue size 1
progress 100% @HLA-DRB1*12:01:01:1, elapsed 1.2s, est remaining 0.0s, peak mem 94MB, user 3.4s, sys 34.0s, output queue size 1689
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: 13269528
reads: 229053
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.034 user 0.007 sys 0.045 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 0.855 user 5.475 sys 6.841 real
calc: 3219322 calls 0.284 user 5.688 sys 6.084 real
done: 1 calls 0.034 user 0.007 sys 0.045 real
execute: 1 calls 0.005 user 0.003 sys 1.239 real
fetch: 3219322 calls 0.290 user 5.869 sys 6.083 real
idle: 74 calls 0.001 user 0.008 sys 31.082 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 146563072 mem 3.542 user 34.586 sys 2.300 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 659_eKx-T1-TDNA-1_A23MHWWLT4_1.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.score --metrics 659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.metrics 659_eKx-T1-TDNA-1_A23MHWWLT4_1.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.1s, est remaining 2.2s, peak mem 252MB, user 0.4s, sys 2.6s, output queue size 6
progress 10% @chr2:76000001, elapsed 0.2s, est remaining 2.0s, peak mem 300MB, user 0.7s, sys 5.2s, output queue size 41
progress 15% @chr3:1, elapsed 0.3s, est remaining 1.8s, peak mem 337MB, user 1.1s, sys 7.8s, output queue size 203
progress 20% @chr3:154000001, elapsed 0.4s, est remaining 1.6s, peak mem 354MB, user 1.5s, sys 10.3s, output queue size 13
progress 25% @chr4:113000001, elapsed 0.5s, est remaining 1.5s, peak mem 361MB, user 1.8s, sys 12.8s, output queue size 21
progress 30% @chr5:88000001, elapsed 0.6s, est remaining 1.4s, peak mem 363MB, user 2.0s, sys 15.3s, output queue size 9
progress 35% @chr6:67000001, elapsed 0.7s, est remaining 1.2s, peak mem 367MB, user 2.3s, sys 17.7s, output queue size 22
progress 40% @chr7:56000001, elapsed 0.8s, est remaining 1.1s, peak mem 372MB, user 2.6s, sys 20.2s, output queue size 9
progress 45% @chr8:60000001, elapsed 0.9s, est remaining 1.0s, peak mem 379MB, user 3.0s, sys 22.6s, output queue size 19
progress 50% @chr9:74000001, elapsed 0.9s, est remaining 0.9s, peak mem 385MB, user 3.3s, sys 25.0s, output queue size 16
progress 55% @chr10:83000001, elapsed 1.0s, est remaining 0.8s, peak mem 387MB, user 3.6s, sys 27.5s, output queue size 12
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.8s, peak mem 387MB, user 4.0s, sys 30.0s, output queue size 21
progress 65% @chr13:16000001, elapsed 1.2s, est remaining 0.7s, peak mem 388MB, user 4.4s, sys 32.5s, output queue size 19
progress 70% @chr14:61000001, elapsed 1.3s, est remaining 0.6s, peak mem 388MB, user 4.6s, sys 35.1s, output queue size 16
progress 75% @chr16:2000001, elapsed 1.4s, est remaining 0.5s, peak mem 394MB, user 5.0s, sys 37.7s, output queue size 15
progress 80% @chr17:81000001, elapsed 1.5s, est remaining 0.4s, peak mem 396MB, user 5.3s, sys 40.3s, output queue size 22
progress 85% @chr20:24000001, elapsed 1.6s, est remaining 0.3s, peak mem 396MB, user 5.7s, sys 42.9s, output queue size 26
progress 90% @chrX:22000001, elapsed 1.7s, est remaining 0.2s, peak mem 397MB, user 6.1s, sys 45.5s, output queue size 10
progress 95% @chrY:26000001, elapsed 1.8s, est remaining 0.1s, peak mem 399MB, user 6.4s, sys 48.0s, output queue size 23
progress 100% @chrUn_JTFH01001912v1_decoy:1, elapsed 1.9s, est remaining 0.0s, peak mem 408MB, user 6.8s, sys 51.4s, output queue size 1091
library 659_eKx-T1-TDNA-1_A23MHWWLT4_1:
chimeric_paired 2893
duped 162626
duped_chimeric_paired 650
duped_paired 162486
duped_unpaired 140
optical_dup 14329
paired 225828
reads 227931
secondary_supplementary 1811
unmapped 1268
unpaired 146
optical dup clusters 6504, maxdup 50, total optical dup pairs 14329
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: 13269528
reads: 229053
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 64053 calls 0.005 user 0.110 sys 0.129 real
MateInfoByVcf::load: 64053 calls 0.984 user 6.040 sys 1.395 real
MateInfoByVcf::parse_events: 64053 calls 0.960 user 5.632 sys 0.862 real
advance: 3219322 calls 0.934 user 5.340 sys 7.462 real
calc: 3219322 calls 1.830 user 16.648 sys 20.388 real
done: 1 calls 0.001 user 0.000 sys 0.006 real
exec_no_coor: 1 calls 0.009 user 0.000 sys 0.010 real
execute: 1 calls 0.000 user 0.000 sys 1.969 real
fetch: 3219323 calls 0.212 user 5.206 sys 6.470 real
find_pairEnds: 64053 calls 0.097 user 0.101 sys 0.194 real
idle: 76 calls 0.022 user 0.035 sys 31.236 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
markDup: 64053 calls 0.257 user 0.280 sys 0.668 real
vcfadvance: 64053 calls 0.023 user 0.143 sys 0.154 real
write: 3219323 calls 0.430 user 5.747 sys 6.449 real
overall: 428105728 mem 7.048 user 52.226 sys 3.012 real