Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/a8653aeebbaef4b9bc8192af461173/.command.sh
  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/3d/9855c5f6faffb82728b335fb87bbda/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/9855c5f6faffb82728b335fb87bbda/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/a8653aeebbaef4b9bc8192af461173/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr1_69091-70008.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:18376800, elapsed 0.3s, est remaining 5.1s, peak mem 79MB, user 0.0s, sys 0.2s, output queue size 866
progress 10% @chr1:37761367, elapsed 0.3s, est remaining 3.0s, peak mem 94MB, user 0.1s, sys 0.3s, output queue size 3518
progress 15% @chr1:65408641, elapsed 0.4s, est remaining 2.3s, peak mem 103MB, user 0.1s, sys 0.5s, output queue size 6248
progress 20% @chr1:113814905, elapsed 0.5s, est remaining 1.8s, peak mem 117MB, user 0.2s, sys 0.8s, output queue size 9006
progress 25% @chr1:155248050, elapsed 0.5s, est remaining 1.5s, peak mem 126MB, user 0.3s, sys 1.0s, output queue size 11349
progress 30% @chr1:179102287, elapsed 0.6s, est remaining 1.3s, peak mem 136MB, user 0.3s, sys 1.3s, output queue size 13823
progress 35% @chr1:209796348, elapsed 0.6s, est remaining 1.1s, peak mem 148MB, user 0.4s, sys 1.5s, output queue size 16253
progress 40% @chr1:246986967, elapsed 0.7s, est remaining 1.0s, peak mem 157MB, user 0.4s, sys 1.8s, output queue size 18658
progress 45% @chr2:32545643, elapsed 0.7s, est remaining 0.9s, peak mem 163MB, user 0.5s, sys 1.9s, output queue size 20944
progress 50% @chr2:74463190, elapsed 0.8s, est remaining 0.8s, peak mem 178MB, user 0.5s, sys 2.2s, output queue size 23433
progress 55% @chr2:113499257, elapsed 0.8s, est remaining 0.7s, peak mem 183MB, user 0.6s, sys 2.4s, output queue size 25966
progress 60% @chr2:171006474, elapsed 0.9s, est remaining 0.6s, peak mem 199MB, user 0.6s, sys 2.6s, output queue size 1711
progress 65% @chr2:202779533, elapsed 0.9s, est remaining 0.5s, peak mem 207MB, user 0.7s, sys 2.9s, output queue size 3980
progress 70% @chr2:233772261, elapsed 1.0s, est remaining 0.4s, peak mem 219MB, user 0.7s, sys 3.1s, output queue size 6459
progress 75% @chr3:25764066, elapsed 1.0s, est remaining 0.3s, peak mem 225MB, user 0.8s, sys 3.3s, output queue size 8712
progress 80% @chr3:49804181, elapsed 1.1s, est remaining 0.3s, peak mem 235MB, user 0.8s, sys 3.5s, output queue size 11160
progress 85% @chr3:101859272, elapsed 1.2s, est remaining 0.2s, peak mem 249MB, user 0.9s, sys 3.8s, output queue size 13793
progress 90% @chr3:139582927, elapsed 1.2s, est remaining 0.1s, peak mem 261MB, user 0.9s, sys 4.1s, output queue size 16390
progress 95% @chr3:187741772, elapsed 1.3s, est remaining 0.1s, peak mem 265MB, user 0.9s, sys 4.3s, output queue size 18803
progress 100% @chr4:13369876, elapsed 1.3s, est remaining 0.0s, peak mem 277MB, user 1.0s, sys 4.6s, output queue size 21033
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71738970
output file size: 22306
reads: 1001089
contig: 49651 intervals 9000373 bases
active: 100735 calls 0.000 user 0.011 sys 0.021 real
advance: 51084 calls 0.010 user 0.019 sys 0.027 real
calc: 100735 calls 0.000 user 0.018 sys 0.021 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.002 sys 2.055 real
fetch: 100735 calls 0.005 user 0.000 sys 0.022 real
fetch_ref: 100735 calls 0.134 user 0.078 sys 0.427 real
idle: 39 calls 0.002 user 0.013 sys 21.499 real
init: 1 calls 0.040 user 0.010 sys 0.051 real
region: 100735 calls 0.000 user 0.005 sys 0.023 real
tracker: 100735 calls 0.066 user 0.014 sys 0.107 real
overall: 291291136 mem 1.580 user 6.466 sys 3.193 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory