Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/2e315391299a4fc8791ce886e00e4f/14862332-cfDNA.bai
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/26/d0c7ccbbd9a0945f92da90f7b58892/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/d0c7ccbbd9a0945f92da90f7b58892/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/2e315391299a4fc8791ce886e00e4f/14862332-cfDNA.bam
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 14862332-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo LocusCollector --fun score_info 14862332-cfDNA.md.score
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:136000001, elapsed 0.1s, est remaining 1.3s, peak mem 72MB, user 0.1s, sys 1.6s, output queue size 28
progress 10% @chr2:76000001, elapsed 0.1s, est remaining 1.2s, peak mem 72MB, user 0.3s, sys 3.4s, output queue size 4
progress 15% @chr2:236000001, elapsed 0.2s, est remaining 1.1s, peak mem 72MB, user 0.4s, sys 5.3s, output queue size 13
progress 20% @chr3:180000001, elapsed 0.3s, est remaining 1.4s, peak mem 72MB, user 0.7s, sys 8.9s, output queue size 30
progress 25% @chr4:108000001, elapsed 0.5s, est remaining 1.4s, peak mem 72MB, user 0.8s, sys 13.2s, output queue size 7
progress 30% @chr5:77000001, elapsed 0.6s, est remaining 1.5s, peak mem 72MB, user 1.0s, sys 17.8s, output queue size 13
progress 35% @chr6:85000001, elapsed 0.8s, est remaining 1.5s, peak mem 72MB, user 1.2s, sys 23.1s, output queue size 56
progress 40% @chr7:49000001, elapsed 1.0s, est remaining 1.5s, peak mem 72MB, user 1.3s, sys 28.7s, output queue size 21
progress 45% @chr8:47000001, elapsed 1.2s, est remaining 1.4s, peak mem 72MB, user 1.6s, sys 34.1s, output queue size 18
progress 50% @chr9:84000001, elapsed 1.4s, est remaining 1.4s, peak mem 72MB, user 1.7s, sys 39.5s, output queue size 6
progress 55% @chr10:89000001, elapsed 1.5s, est remaining 1.3s, peak mem 72MB, user 1.9s, sys 44.6s, output queue size 6
progress 60% @chr11:115000001, elapsed 1.7s, est remaining 1.1s, peak mem 72MB, user 2.1s, sys 49.6s, output queue size 11
progress 65% @chr13:10000001, elapsed 1.9s, est remaining 1.0s, peak mem 72MB, user 2.3s, sys 54.9s, output queue size 5
progress 70% @chr14:57000001, elapsed 2.0s, est remaining 0.9s, peak mem 72MB, user 2.4s, sys 60.0s, output queue size 7
progress 75% @chr16:10000001, elapsed 2.2s, est remaining 0.7s, peak mem 72MB, user 2.7s, sys 65.0s, output queue size 4
progress 80% @chr18:19000001, elapsed 2.4s, est remaining 0.6s, peak mem 72MB, user 2.9s, sys 69.9s, output queue size 5
progress 85% @chr20:41000001, elapsed 2.6s, est remaining 0.5s, peak mem 72MB, user 3.2s, sys 75.1s, output queue size 12
progress 90% @chrX:42000001, elapsed 2.7s, est remaining 0.3s, peak mem 72MB, user 3.3s, sys 80.6s, output queue size 9
progress 95% @chrY:41000001, elapsed 2.9s, est remaining 0.2s, peak mem 72MB, user 3.6s, sys 86.0s, output queue size 9
progress 100% @HLA-DRB1*09:21:1, elapsed 3.1s, est remaining 0.0s, peak mem 72MB, user 3.7s, sys 91.3s, output queue size 25
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 384
algo: LocusCollector
license: sentieon:Dedup=31
input file size: 33467
reads: 0
contig: 3367 intervals 3217346917 bases
LocusCollector::merge: 1 calls 0.002 user 0.000 sys 0.003 real
advance: 3219322 calls 0.265 user 15.081 sys 15.901 real
calc: 3219322 calls 0.287 user 15.795 sys 15.523 real
done: 1 calls 0.002 user 0.000 sys 0.003 real
execute: 1 calls 0.001 user 0.001 sys 3.100 real
fetch: 3219322 calls 0.288 user 15.168 sys 15.410 real
idle: 79 calls 0.001 user 0.002 sys 31.158 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 75653120 mem 3.813 user 92.108 sys 4.174 real
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -i 14862332-cfDNA.bam -r Homo_sapiens_assembly38.fasta --algo Dedup --score_info 14862332-cfDNA.md.score --metrics 14862332-cfDNA.md.metrics 14862332-cfDNA.md.bam
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:162000001, elapsed 0.1s, est remaining 2.3s, peak mem 84MB, user 0.3s, sys 2.8s, output queue size 9
progress 10% @chr2:75000001, elapsed 0.2s, est remaining 2.0s, peak mem 84MB, user 0.7s, sys 5.5s, output queue size 13
progress 15% @chr2:236000001, elapsed 0.3s, est remaining 1.8s, peak mem 84MB, user 1.0s, sys 8.3s, output queue size 11
progress 20% @chr3:156000001, elapsed 0.4s, est remaining 1.7s, peak mem 84MB, user 1.3s, sys 11.0s, output queue size 16
progress 25% @chr4:118000001, elapsed 0.5s, est remaining 1.6s, peak mem 84MB, user 1.7s, sys 13.5s, output queue size 5
progress 30% @chr5:87000001, elapsed 0.6s, est remaining 1.4s, peak mem 84MB, user 2.1s, sys 16.3s, output queue size 18
progress 35% @chr6:69000001, elapsed 0.7s, est remaining 1.3s, peak mem 84MB, user 2.4s, sys 19.0s, output queue size 10
progress 40% @chr7:57000001, elapsed 0.8s, est remaining 1.2s, peak mem 84MB, user 2.9s, sys 21.5s, output queue size 6
progress 45% @chr8:51000001, elapsed 1.0s, est remaining 1.2s, peak mem 87MB, user 3.3s, sys 25.4s, output queue size 6
progress 50% @chr9:98000001, elapsed 1.1s, est remaining 1.1s, peak mem 87MB, user 3.8s, sys 30.5s, output queue size 25
progress 55% @chr10:91000001, elapsed 1.3s, est remaining 1.1s, peak mem 87MB, user 4.4s, sys 35.8s, output queue size 18
progress 60% @chr11:109000001, elapsed 1.6s, est remaining 1.1s, peak mem 87MB, user 5.3s, sys 42.9s, output queue size 14
progress 65% @chr13:9000001, elapsed 1.9s, est remaining 1.0s, peak mem 87MB, user 6.0s, sys 50.5s, output queue size 28
progress 70% @chr14:54000001, elapsed 2.1s, est remaining 0.9s, peak mem 87MB, user 6.8s, sys 58.3s, output queue size 21
progress 75% @chr16:8000001, elapsed 2.4s, est remaining 0.8s, peak mem 87MB, user 7.4s, sys 66.0s, output queue size 73
progress 80% @chr18:9000001, elapsed 2.7s, est remaining 0.7s, peak mem 87MB, user 8.1s, sys 73.9s, output queue size 13
progress 85% @chr20:22000001, elapsed 3.0s, est remaining 0.5s, peak mem 87MB, user 8.8s, sys 81.4s, output queue size 9
progress 90% @chrX:20000001, elapsed 3.2s, est remaining 0.4s, peak mem 87MB, user 9.5s, sys 88.6s, output queue size 1
progress 95% @chrY:28000001, elapsed 3.5s, est remaining 0.2s, peak mem 87MB, user 10.3s, sys 95.5s, output queue size 13
progress 100% @HLA-DQA1*06:01:01:1, elapsed 3.9s, est remaining 0.0s, peak mem 110MB, user 14.5s, sys 105.2s, output queue size 46
library 14862332-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: 000a06d1
features: 1f8bfbff fffab20b
extended: f1bf27eb 1b407f7e
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: Dedup
license: sentieon:Dedup=31
input file size: 33467
reads: 0
contig: 3367 intervals 3217346917 bases
advance: 3219322 calls 0.439 user 11.627 sys 13.081 real
calc: 3219322 calls 1.831 user 37.776 sys 39.545 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
exec_no_coor: 1 calls 0.009 user 0.000 sys 0.012 real
execute: 1 calls 0.001 user 0.001 sys 3.933 real
fetch: 3219322 calls 0.374 user 13.074 sys 12.900 real
idle: 84 calls 0.020 user 0.033 sys 31.245 real
init: 1 calls 0.009 user 0.001 sys 0.006 real
write: 3219322 calls 0.573 user 12.376 sys 12.997 real
overall: 116342784 mem 15.147 user 106.666 sys 5.003 real