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/c3/5506df0a357cd11929604eb852eb91/Sig_18_tissue.md.bam.bai
  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/c3/5506df0a357cd11929604eb852eb91/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/04/fe79dc4decaa10f21287c5cb71f63b/.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/04/fe79dc4decaa10f21287c5cb71f63b/.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 Sig_18_tissue.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 Sig_18_tissue.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119911554, elapsed 0.0s, est remaining 0.8s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 3013
progress 10% @chr2:20034967, elapsed 0.1s, est remaining 0.8s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 3938
progress 15% @chr2:189050569, elapsed 0.1s, est remaining 0.7s, peak mem 181MB, user 0.0s, sys 0.0s, output queue size 14340
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 3086
progress 25% @chr4:88046642, elapsed 0.2s, est remaining 0.6s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 13343
progress 30% @chr5:147395559, elapsed 0.2s, est remaining 0.6s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 23380
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 33350
progress 40% @chr7:128812708, elapsed 0.3s, est remaining 0.5s, peak mem 217MB, user 0.0s, sys 0.0s, output queue size 42816
progress 45% @chr9:977002, elapsed 0.4s, est remaining 0.4s, peak mem 371MB, user 0.0s, sys 0.0s, output queue size 52186
progress 50% @chr10:32543300, elapsed 0.4s, est remaining 0.4s, peak mem 418MB, user 0.0s, sys 0.1s, output queue size 1631
progress 55% @chr11:48216810, elapsed 0.4s, est remaining 0.4s, peak mem 454MB, user 0.0s, sys 0.1s, output queue size 12093
progress 60% @chr12:21912872, elapsed 0.5s, est remaining 0.3s, peak mem 454MB, user 0.0s, sys 0.1s, output queue size 21642
progress 65% @chr13:49255839, elapsed 0.5s, est remaining 0.3s, peak mem 479MB, user 0.0s, sys 0.1s, output queue size 32696
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.2s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 42735
progress 75% @chr16:30893212, elapsed 0.6s, est remaining 0.2s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 52292
progress 80% @chr17:42483038, elapsed 0.6s, est remaining 0.2s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 62983
progress 85% @chr19:5679345, elapsed 0.7s, est remaining 0.1s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 73392
progress 90% @chr19:55731999, elapsed 0.7s, est remaining 0.1s, peak mem 509MB, user 0.0s, sys 0.1s, output queue size 82891
progress 95% @chr22:37069073, elapsed 1.2s, est remaining 0.1s, peak mem 2516MB, user 8.5s, sys 1.7s, output queue size 3244
progress 100% @chrY:24862062, elapsed 1.2s, est remaining 0.0s, peak mem 2516MB, user 8.8s, sys 1.7s, output queue size 2632
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: 50047053
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.829 user 0.113 sys 2.299 real
done: 1 calls 0.256 user 0.049 sys 0.312 real
execute: 1 calls 0.006 user 0.001 sys 1.204 real
fetch_reads: 208647 calls 0.079 user 0.001 sys 0.179 real
fetch_ref: 2079 calls 0.015 user 0.011 sys 0.017 real
fetch_vcf: 2079 calls 0.821 user 0.031 sys 1.055 real
idle: 92 calls 0.001 user 0.002 sys 31.595 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 7.303 user 1.564 sys 9.137 real
overall: 2639032320 mem 12.658 user 8.901 sys 2.564 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