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-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/52/33b8c34be7b42e0c78b1bbe3251224/1136_4XR-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8f/0ba14c0b92ae97e073509e78a31339/.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/8f/0ba14c0b92ae97e073509e78a31339/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/33b8c34be7b42e0c78b1bbe3251224/1136_4XR-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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 1136_4XR-T1-TDNA-1_A23MHWWLT4_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 1136_4XR-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:120034628, elapsed 8.9s, est remaining 169.5s, peak mem 5430MB, user 235.8s, sys 5.8s, output queue size 171
progress 10% @chr2:23691674, elapsed 17.5s, est remaining 157.4s, peak mem 6551MB, user 464.9s, sys 8.4s, output queue size 1153
progress 15% @chr2:190249640, elapsed 26.0s, est remaining 147.6s, peak mem 7039MB, user 694.8s, sys 10.7s, output queue size 287
progress 20% @chr3:98592949, elapsed 34.4s, est remaining 137.5s, peak mem 7113MB, user 918.6s, sys 13.0s, output queue size 419
progress 25% @chr4:88470614, elapsed 41.6s, est remaining 124.9s, peak mem 7185MB, user 1109.1s, sys 14.3s, output queue size 99
progress 30% @chr5:147824661, elapsed 47.8s, est remaining 111.6s, peak mem 7357MB, user 1271.0s, sys 16.0s, output queue size 206
progress 35% @chr6:131700469, elapsed 57.3s, est remaining 106.4s, peak mem 7544MB, user 1524.3s, sys 17.9s, output queue size 639
progress 40% @chr7:128942082, elapsed 67.0s, est remaining 100.4s, peak mem 8234MB, user 1776.5s, sys 19.8s, output queue size 1471
progress 45% @chr9:977002, elapsed 76.1s, est remaining 93.1s, peak mem 8234MB, user 2030.7s, sys 21.6s, output queue size 151
progress 50% @chr10:34337275, elapsed 85.1s, est remaining 85.1s, peak mem 8342MB, user 2274.3s, sys 23.2s, output queue size 109
progress 55% @chr11:48216810, elapsed 92.1s, est remaining 75.3s, peak mem 8342MB, user 2459.1s, sys 24.3s, output queue size 17
progress 60% @chr12:11810159, elapsed 100.5s, est remaining 67.0s, peak mem 8342MB, user 2682.8s, sys 25.7s, output queue size 794
progress 65% @chr13:49476476, elapsed 108.0s, est remaining 58.2s, peak mem 8342MB, user 2887.7s, sys 27.1s, output queue size 569
progress 70% @chr15:42449771, elapsed 115.7s, est remaining 49.6s, peak mem 8342MB, user 3092.5s, sys 28.4s, output queue size 459
progress 75% @chr16:30927308, elapsed 125.4s, est remaining 41.8s, peak mem 8342MB, user 3359.2s, sys 30.4s, output queue size 34
progress 80% @chr17:42317112, elapsed 135.2s, est remaining 33.8s, peak mem 8342MB, user 3627.7s, sys 32.0s, output queue size 709
progress 85% @chr19:5739326, elapsed 143.5s, est remaining 25.3s, peak mem 8342MB, user 3856.1s, sys 33.6s, output queue size 404
progress 90% @chr19:55358145, elapsed 151.0s, est remaining 16.8s, peak mem 8342MB, user 4059.2s, sys 35.0s, output queue size 127
progress 95% @chr22:36505896, elapsed 160.3s, est remaining 8.4s, peak mem 8538MB, user 4310.2s, sys 36.9s, output queue size 27
progress 100% @chrX:156004420, elapsed 169.0s, est remaining 0.0s, peak mem 8716MB, user 4544.8s, sys 38.4s, output queue size 562
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: 61364023637
reads: 1205609827
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2317.112 user 30.181 sys 2436.440 real
done: 1 calls 0.406 user 0.306 sys 0.715 real
execute: 1 calls 0.004 user 0.011 sys 168.989 real
fetch_reads: 208647 calls 206.100 user 0.319 sys 213.420 real
fetch_ref: 207085 calls 1.139 user 1.056 sys 2.137 real
fetch_vcf: 207085 calls 80.923 user 2.198 sys 86.139 real
idle: 115 calls 0.203 user 0.000 sys 32.156 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 474424 calls 2307.989 user 3.177 sys 2375.910 real
overall: 9140305920 mem 5106.148 user 39.766 sys 170.582 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