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/7e/ab3819dac8754631e777fe56aa0a7f/1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.bam.bai
  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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7e/ab3819dac8754631e777fe56aa0a7f/1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/cf2d4690fd425e9714b3725fe7f31d/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b2/cf2d4690fd425e9714b3725fe7f31d/.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 (13 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.md.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo QualCal -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz 1029_BICJ-N1-BDNA-1_B23KGCJLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 3.1s, est remaining 58.0s, peak mem 3294MB, user 77.0s, sys 2.6s, output queue size 172
progress 10% @chr2:21001730, elapsed 5.7s, est remaining 51.1s, peak mem 3601MB, user 143.3s, sys 3.3s, output queue size 652
progress 15% @chr2:190360103, elapsed 8.9s, est remaining 50.7s, peak mem 3742MB, user 223.2s, sys 4.2s, output queue size 450
progress 20% @chr3:98817769, elapsed 12.3s, est remaining 49.2s, peak mem 3850MB, user 308.0s, sys 5.2s, output queue size 429
progress 25% @chr4:80286325, elapsed 14.9s, est remaining 44.7s, peak mem 3850MB, user 372.8s, sys 6.0s, output queue size 540
progress 30% @chr5:147639632, elapsed 17.2s, est remaining 40.2s, peak mem 3860MB, user 430.1s, sys 6.6s, output queue size 195
progress 35% @chr6:131890341, elapsed 20.5s, est remaining 38.1s, peak mem 4101MB, user 512.2s, sys 7.5s, output queue size 637
progress 40% @chr7:128815614, elapsed 24.1s, est remaining 36.2s, peak mem 4162MB, user 595.2s, sys 8.5s, output queue size 543
progress 45% @chr9:116800, elapsed 27.9s, est remaining 34.1s, peak mem 4190MB, user 692.9s, sys 9.8s, output queue size 87
progress 50% @chr10:32925871, elapsed 31.2s, est remaining 31.2s, peak mem 4206MB, user 776.0s, sys 10.6s, output queue size 107
progress 55% @chr11:48144675, elapsed 33.9s, est remaining 27.7s, peak mem 4206MB, user 845.3s, sys 11.1s, output queue size 9
progress 60% @chr12:23740867, elapsed 37.2s, est remaining 24.8s, peak mem 4206MB, user 926.8s, sys 11.8s, output queue size 706
progress 65% @chr13:49534122, elapsed 40.3s, est remaining 21.7s, peak mem 4206MB, user 1004.7s, sys 12.4s, output queue size 566
progress 70% @chr15:42736302, elapsed 43.2s, est remaining 18.5s, peak mem 4206MB, user 1078.5s, sys 13.0s, output queue size 455
progress 75% @chr16:30930073, elapsed 46.7s, est remaining 15.6s, peak mem 4206MB, user 1167.4s, sys 13.8s, output queue size 33
progress 80% @chr17:42685217, elapsed 50.2s, est remaining 12.6s, peak mem 4206MB, user 1260.6s, sys 14.8s, output queue size 698
progress 85% @chr19:5693552, elapsed 53.4s, est remaining 9.4s, peak mem 4206MB, user 1339.5s, sys 15.6s, output queue size 404
progress 90% @chr19:55772602, elapsed 56.4s, est remaining 6.3s, peak mem 4206MB, user 1416.9s, sys 16.2s, output queue size 103
progress 95% @chr22:36587465, elapsed 59.8s, est remaining 3.1s, peak mem 4277MB, user 1501.3s, sys 17.0s, output queue size 12
progress 100% @chr6_GL000251v2_alt:3939000, elapsed 62.9s, est remaining 0.0s, peak mem 4294MB, user 1579.3s, sys 17.6s, output queue size 7
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: QualCal
license: sentieon:QualCal=31
input file size: 17911741621
reads: 361302612
contig: 201779 intervals 37922265 bases
advance: 208647 calls 707.913 user 11.114 sys 747.888 real
done: 1 calls 0.347 user 0.492 sys 0.848 real
execute: 1 calls 0.002 user 0.011 sys 62.904 real
fetch_reads: 208647 calls 50.134 user 0.158 sys 53.220 real
fetch_ref: 206949 calls 1.095 user 0.701 sys 1.714 real
fetch_vcf: 206949 calls 79.176 user 2.152 sys 83.591 real
idle: 108 calls 0.136 user 0.014 sys 32.190 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 294068 calls 987.103 user 3.463 sys 1021.744 real
overall: 4502650880 mem 1900.806 user 19.258 sys 64.352 real
ls: cannot access '*.table.post': No such file or directory
ls: cannot access '*.recalibrated.bam': No such file or directory
ls: cannot access '*.recalibrated.bam.bai': No such file or directory
ls: cannot access '*.csv': No such file or directory
ls: cannot access '*.pdf': No such file or directory