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/f6/e85c545123b110e37a50a4fc5e7dbd/Sig_18_Blood.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/458be8b691dfd1cf6ffeb1d6f3b0ba/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6b/458be8b691dfd1cf6ffeb1d6f3b0ba/.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/f6/e85c545123b110e37a50a4fc5e7dbd/Sig_18_Blood.bam
==> STAGING COMPLETE (6 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_Blood.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info Sig_18_Blood.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:160000001, elapsed 0.1s, est remaining 1.3s, peak mem 81MB, user 0.1s, sys 1.5s, output queue size 17
progress 10% @chr2:74000001, elapsed 0.1s, est remaining 1.2s, peak mem 81MB, user 0.3s, sys 3.2s, output queue size 3
progress 15% @chr2:235000001, elapsed 0.2s, est remaining 1.1s, peak mem 81MB, user 0.5s, sys 4.9s, output queue size 11
progress 20% @chr3:153000001, elapsed 0.3s, est remaining 1.0s, peak mem 81MB, user 0.7s, sys 6.7s, output queue size 11
progress 25% @chr4:116000001, elapsed 0.3s, est remaining 0.9s, peak mem 81MB, user 0.8s, sys 8.5s, output queue size 19
progress 30% @chr5:86000001, elapsed 0.4s, est remaining 0.9s, peak mem 81MB, user 0.9s, sys 10.2s, output queue size 16
progress 35% @chr6:63000001, elapsed 0.4s, est remaining 0.8s, peak mem 81MB, user 1.0s, sys 12.0s, output queue size 20
progress 40% @chr7:53000001, elapsed 0.5s, est remaining 0.8s, peak mem 81MB, user 1.2s, sys 13.8s, output queue size 2
progress 45% @chr8:58000001, elapsed 0.6s, est remaining 0.7s, peak mem 81MB, user 1.2s, sys 15.6s, output queue size 6
progress 50% @chr9:73000001, elapsed 0.6s, est remaining 0.6s, peak mem 81MB, user 1.4s, sys 17.3s, output queue size 6
progress 55% @chr10:94000001, elapsed 0.7s, est remaining 0.6s, peak mem 81MB, user 1.6s, sys 19.0s, output queue size 13
progress 60% @chr11:123000001, elapsed 0.7s, est remaining 0.5s, peak mem 81MB, user 1.8s, sys 20.7s, output queue size 21
progress 65% @chr13:15000001, elapsed 0.8s, est remaining 0.4s, peak mem 81MB, user 1.9s, sys 22.5s, output queue size 8
progress 70% @chr14:60000001, elapsed 0.9s, est remaining 0.4s, peak mem 81MB, user 2.0s, sys 24.3s, output queue size 12
progress 75% @chr16:14000001, elapsed 0.9s, est remaining 0.3s, peak mem 81MB, user 2.1s, sys 26.1s, output queue size 17
progress 80% @chr18:1, elapsed 1.0s, est remaining 0.2s, peak mem 81MB, user 2.3s, sys 27.9s, output queue size 6
progress 85% @chr20:23000001, elapsed 1.1s, est remaining 0.2s, peak mem 81MB, user 2.5s, sys 29.6s, output queue size 13
progress 90% @chrX:33000001, elapsed 1.1s, est remaining 0.1s, peak mem 126MB, user 3.0s, sys 31.1s, output queue size 114
progress 95% @chrY:31000001, elapsed 1.2s, est remaining 0.1s, peak mem 154MB, user 3.4s, sys 33.0s, output queue size 276
progress 100% @chr21:41000001, elapsed 1.5s, est remaining 0.0s, peak mem 184MB, user 4.1s, sys 35.8s, output queue size 3664
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.019 user 0.015 sys 0.046 real
VcfLineRecordHelper::sort: 31 calls 0.000 user 0.000 sys 0.000 real
advance: 3219322 calls 1.428 user 7.287 sys 8.597 real
calc: 3219322 calls 0.317 user 5.443 sys 6.411 real
done: 1 calls 0.019 user 0.015 sys 0.046 real
execute: 1 calls 0.002 user 0.005 sys 1.497 real
fetch: 3219322 calls 0.462 user 5.770 sys 6.334 real
idle: 73 calls 0.009 user 0.019 sys 36.468 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 235491328 mem 4.295 user 36.382 sys 2.557 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i Sig_18_Blood.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info Sig_18_Blood.md.score --metrics Sig_18_Blood.md.metrics Sig_18_Blood.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:157000001, elapsed 0.1s, est remaining 2.2s, peak mem 184MB, user 0.5s, sys 2.4s, output queue size 13
progress 10% @chr2:73000001, elapsed 0.2s, est remaining 1.8s, peak mem 213MB, user 0.7s, sys 4.8s, output queue size 5
progress 15% @chr2:232000001, elapsed 0.3s, est remaining 1.6s, peak mem 237MB, user 0.9s, sys 7.3s, output queue size 19
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.5s, peak mem 255MB, user 1.1s, sys 9.7s, output queue size 3
progress 25% @chr4:114000001, elapsed 0.5s, est remaining 1.4s, peak mem 262MB, user 1.5s, sys 12.0s, output queue size 16
progress 30% @chr5:81000001, elapsed 0.5s, est remaining 1.3s, peak mem 270MB, user 1.8s, sys 14.4s, output queue size 8
progress 35% @chr6:64000001, elapsed 0.6s, est remaining 1.2s, peak mem 279MB, user 2.2s, sys 16.7s, output queue size 3
progress 40% @chr7:57000001, elapsed 0.7s, est remaining 1.1s, peak mem 285MB, user 2.4s, sys 19.0s, output queue size 16
progress 45% @chr8:37000001, elapsed 0.8s, est remaining 1.0s, peak mem 286MB, user 2.7s, sys 21.4s, output queue size 22
progress 50% @chr9:74000001, elapsed 0.9s, est remaining 0.9s, peak mem 300MB, user 3.0s, sys 23.8s, output queue size 1
progress 55% @chr10:91000001, elapsed 1.0s, est remaining 0.8s, peak mem 300MB, user 3.3s, sys 26.1s, output queue size 4
progress 60% @chr11:123000001, elapsed 1.1s, est remaining 0.7s, peak mem 304MB, user 3.7s, sys 28.4s, output queue size 8
progress 65% @chr13:15000001, elapsed 1.1s, est remaining 0.6s, peak mem 307MB, user 4.0s, sys 30.8s, output queue size 4
progress 70% @chr14:63000001, elapsed 1.2s, est remaining 0.5s, peak mem 310MB, user 4.3s, sys 33.1s, output queue size 6
progress 75% @chr16:16000001, elapsed 1.3s, est remaining 0.4s, peak mem 312MB, user 4.6s, sys 35.6s, output queue size 12
progress 80% @chr18:2000001, elapsed 1.4s, est remaining 0.4s, peak mem 313MB, user 4.9s, sys 38.0s, output queue size 22
progress 85% @chr20:23000001, elapsed 1.5s, est remaining 0.3s, peak mem 313MB, user 5.2s, sys 40.4s, output queue size 13
progress 90% @chrX:39000001, elapsed 1.7s, est remaining 0.2s, peak mem 531MB, user 7.2s, sys 41.7s, output queue size 114
progress 95% @chrY:29000001, elapsed 1.8s, est remaining 0.1s, peak mem 547MB, user 9.0s, sys 42.7s, output queue size 276
progress 100% @chr21:41000001, elapsed 2.9s, est remaining 0.0s, peak mem 582MB, user 14.6s, sys 44.8s, output queue size 3664
library Sig_18_Blood:
chimeric_paired 1027
duped 115575
duped_chimeric_paired 2
duped_paired 115574
duped_unpaired 1
optical_dup 5956
paired 999968
reads 1001133
secondary_supplementary 1151
unmapped 7
unpaired 7
optical dup clusters 5759, maxdup 3, total optical dup pairs 5956
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51298918
reads: 1001133
contig: 3367 intervals 3217346917 bases
MateInfoByVcf::buildInfoMap: 26026 calls 0.010 user 0.000 sys 0.022 real
MateInfoByVcf::load: 26026 calls 4.568 user 0.754 sys 3.912 real
MateInfoByVcf::parse_events: 26026 calls 4.496 user 0.669 sys 3.804 real
advance: 3219322 calls 1.017 user 5.266 sys 7.072 real
calc: 3219322 calls 4.658 user 16.284 sys 21.216 real
done: 1 calls 0.002 user 0.000 sys 0.003 real
exec_no_coor: 1 calls 0.000 user 0.000 sys 0.000 real
execute: 1 calls 0.002 user 0.001 sys 2.995 real
fetch: 3219322 calls 0.418 user 5.104 sys 6.112 real
find_pairEnds: 26026 calls 0.134 user 0.012 sys 0.338 real
idle: 1767 calls 0.116 user 0.167 sys 61.256 real
init: 1 calls 0.010 user 0.000 sys 0.006 real
markDup: 26026 calls 0.676 user 0.065 sys 1.270 real
vcfadvance: 26026 calls 0.017 user 0.097 sys 0.041 real
write: 3219322 calls 2.443 user 5.487 sys 7.650 real
overall: 610557952 mem 15.339 user 45.658 sys 4.016 real