Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/0547ecd05b03810f5c43ebec19feb1/13929215-cfDNA.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/e5/9928b415a25e9b143a567745a14137/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/9928b415a25e9b143a567745a14137/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/07/0547ecd05b03810f5c43ebec19feb1/13929215-cfDNA.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 13929215-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 13929215-cfDNA.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:172000001, elapsed 0.1s, est remaining 1.3s, peak mem 79MB, user 0.1s, sys 1.6s, output queue size 21
progress 10% @chr2:84000001, elapsed 0.1s, est remaining 1.2s, peak mem 79MB, user 0.2s, sys 3.4s, output queue size 17
progress 15% @chr3:1000001, elapsed 0.2s, est remaining 1.1s, peak mem 79MB, user 0.3s, sys 5.2s, output queue size 19
progress 20% @chr3:134000001, elapsed 0.3s, est remaining 1.0s, peak mem 79MB, user 0.4s, sys 7.1s, output queue size 23
progress 25% @chr4:126000001, elapsed 0.3s, est remaining 1.0s, peak mem 79MB, user 0.6s, sys 8.9s, output queue size 16
progress 30% @chr5:96000001, elapsed 0.4s, est remaining 0.9s, peak mem 79MB, user 0.7s, sys 10.6s, output queue size 16
progress 35% @chr6:76000001, elapsed 0.4s, est remaining 0.8s, peak mem 79MB, user 0.8s, sys 12.5s, output queue size 24
progress 40% @chr7:68000001, elapsed 0.5s, est remaining 0.8s, peak mem 79MB, user 1.0s, sys 14.2s, output queue size 21
progress 45% @chr8:33000001, elapsed 0.6s, est remaining 0.7s, peak mem 79MB, user 1.1s, sys 16.0s, output queue size 24
progress 50% @chr9:87000001, elapsed 0.6s, est remaining 0.6s, peak mem 79MB, user 1.2s, sys 17.8s, output queue size 22
progress 55% @chr10:77000001, elapsed 0.7s, est remaining 0.6s, peak mem 79MB, user 1.4s, sys 19.6s, output queue size 18
progress 60% @chr12:1000001, elapsed 0.8s, est remaining 0.5s, peak mem 79MB, user 1.5s, sys 21.3s, output queue size 23
progress 65% @chr12:125000001, elapsed 0.8s, est remaining 0.4s, peak mem 79MB, user 1.6s, sys 23.2s, output queue size 24
progress 70% @chr14:47000001, elapsed 0.9s, est remaining 0.4s, peak mem 79MB, user 1.7s, sys 24.9s, output queue size 14
progress 75% @chr15:101000001, elapsed 0.9s, est remaining 0.3s, peak mem 79MB, user 1.8s, sys 26.7s, output queue size 16
progress 80% @chr18:7000001, elapsed 1.0s, est remaining 0.3s, peak mem 79MB, user 1.9s, sys 28.5s, output queue size 20
progress 85% @chr20:37000001, elapsed 1.1s, est remaining 0.2s, peak mem 79MB, user 2.0s, sys 30.3s, output queue size 18
progress 90% @chrX:6000001, elapsed 1.1s, est remaining 0.1s, peak mem 79MB, user 2.2s, sys 32.2s, output queue size 15
progress 95% @chrY:32000001, elapsed 1.2s, est remaining 0.1s, peak mem 79MB, user 2.3s, sys 33.9s, output queue size 9
progress 100% @HLA-DQB1*06:09:01:1, elapsed 1.3s, est remaining 0.0s, peak mem 79MB, user 2.5s, sys 35.4s, output queue size 106
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000c06f2
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 33468
reads: 0
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.000 user 0.000 sys 0.003 real
advance: 3219322 calls 0.239 user 5.471 sys 6.083 real
calc: 3219322 calls 0.212 user 6.049 sys 5.990 real
done: 1 calls 0.000 user 0.000 sys 0.003 real
execute: 1 calls 0.002 user 0.004 sys 1.259 real
fetch: 3219322 calls 0.151 user 6.145 sys 5.986 real
idle: 73 calls 0.001 user 0.002 sys 31.120 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 83656704 mem 2.597 user 35.883 sys 2.319 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 13929215-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 13929215-cfDNA.md.score --metrics 13929215-cfDNA.md.metrics 13929215-cfDNA.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:159000001, elapsed 0.1s, est remaining 2.0s, peak mem 132MB, user 0.2s, sys 2.4s, output queue size 5
progress 10% @chr2:90000001, elapsed 0.2s, est remaining 1.7s, peak mem 132MB, user 0.6s, sys 4.7s, output queue size 3
progress 15% @chr2:235000001, elapsed 0.3s, est remaining 1.5s, peak mem 132MB, user 0.9s, sys 7.1s, output queue size 28
progress 20% @chr3:152000001, elapsed 0.4s, est remaining 1.4s, peak mem 133MB, user 1.2s, sys 9.4s, output queue size 2
progress 25% @chr4:116000001, elapsed 0.4s, est remaining 1.3s, peak mem 134MB, user 1.4s, sys 11.8s, output queue size 3
progress 30% @chr5:83000001, elapsed 0.5s, est remaining 1.2s, peak mem 134MB, user 1.7s, sys 14.2s, output queue size 3
progress 35% @chr6:63000001, elapsed 0.6s, est remaining 1.1s, peak mem 134MB, user 2.1s, sys 16.6s, output queue size 2
progress 40% @chr7:53000001, elapsed 0.7s, est remaining 1.1s, peak mem 134MB, user 2.4s, sys 18.9s, output queue size 2
progress 45% @chr8:56000001, elapsed 0.8s, est remaining 1.0s, peak mem 134MB, user 2.7s, sys 21.3s, output queue size 26
progress 50% @chr9:70000001, elapsed 0.9s, est remaining 0.9s, peak mem 134MB, user 3.0s, sys 23.6s, output queue size 5
progress 55% @chr10:90000001, elapsed 1.0s, est remaining 0.8s, peak mem 134MB, user 3.5s, sys 25.8s, output queue size 5
progress 60% @chr11:116000001, elapsed 1.0s, est remaining 0.7s, peak mem 134MB, user 3.7s, sys 28.2s, output queue size 7
progress 65% @chr13:11000001, elapsed 1.1s, est remaining 0.6s, peak mem 134MB, user 4.1s, sys 30.5s, output queue size 23
progress 70% @chr14:81000001, elapsed 1.2s, est remaining 0.5s, peak mem 134MB, user 4.4s, sys 32.8s, output queue size 6
progress 75% @chr15:83000001, elapsed 1.3s, est remaining 0.4s, peak mem 134MB, user 4.6s, sys 35.2s, output queue size 32
progress 80% @chr17:74000001, elapsed 1.4s, est remaining 0.3s, peak mem 134MB, user 4.9s, sys 37.5s, output queue size 10
progress 85% @chr20:12000001, elapsed 1.5s, est remaining 0.3s, peak mem 134MB, user 5.2s, sys 39.8s, output queue size 28
progress 90% @chrX:9000001, elapsed 1.6s, est remaining 0.2s, peak mem 134MB, user 5.6s, sys 42.0s, output queue size 12
progress 95% @chrY:38000001, elapsed 1.6s, est remaining 0.1s, peak mem 134MB, user 6.0s, sys 44.2s, output queue size 11
progress 100% @HLA-DRB1*15:03:01:01:1, elapsed 1.9s, est remaining 0.0s, peak mem 134MB, user 6.9s, sys 49.0s, output queue size 372
library 13929215-cfDNA:
optical dup clusters 0, maxdup 0, total optical dup pairs 0
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000c06f2
features: bfebfbff 7ffefbff
extended: f3bfb7ef fb417ffe
amd bits: 2c100800 00000121
brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: Dedup
license: sentieon:Dedup=31
input file size: 33468
reads: 0
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 0.227 user 5.194 sys 5.701 real
calc: 3219322 calls 1.211 user 16.111 sys 17.723 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
exec_no_coor: 1 calls 0.000 user 0.005 sys 0.004 real
execute: 1 calls 0.003 user 0.005 sys 1.881 real
fetch: 3219322 calls 0.209 user 5.503 sys 5.668 real
idle: 86 calls 0.004 user 0.072 sys 31.226 real
init: 1 calls 0.000 user 0.000 sys 0.006 real
write: 3219322 calls 0.325 user 5.508 sys 5.796 real
overall: 141385728 mem 7.005 user 49.666 sys 2.932 real