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/3f/1da352571a0470ddf30af8993404ce/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.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-rnd-pltf-dev-nextflow-scratch-01/work/3f/1da352571a0470ddf30af8993404ce/FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.md.bam
  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/8e/38e5e267b66aa2207b2ef98bf07b04/.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/8e/38e5e267b66aa2207b2ef98bf07b04/.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 FFPE_HD789_01_p2_gDNA_01_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 FFPE_HD789_01_p2_gDNA_01_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 9.6s, est remaining 183.2s, peak mem 5195MB, user 253.0s, sys 4.9s, output queue size 181
progress 10% @chr2:23695623, elapsed 19.1s, est remaining 171.5s, peak mem 7005MB, user 498.6s, sys 7.8s, output queue size 660
progress 15% @chr2:190062224, elapsed 28.9s, est remaining 163.9s, peak mem 7909MB, user 759.3s, sys 11.2s, output queue size 297
progress 20% @chr3:98591012, elapsed 39.0s, est remaining 155.9s, peak mem 8016MB, user 1030.0s, sys 13.0s, output queue size 415
progress 25% @chr4:88500915, elapsed 47.1s, est remaining 141.3s, peak mem 8281MB, user 1240.0s, sys 14.6s, output queue size 88
progress 30% @chr5:147644058, elapsed 53.9s, est remaining 125.8s, peak mem 8281MB, user 1415.7s, sys 16.0s, output queue size 209
progress 35% @chr6:131700469, elapsed 65.2s, est remaining 121.0s, peak mem 8569MB, user 1713.3s, sys 18.5s, output queue size 640
progress 40% @chr7:102248412, elapsed 78.0s, est remaining 117.0s, peak mem 9117MB, user 2047.0s, sys 20.7s, output queue size 1432
progress 45% @chr9:2104003, elapsed 91.1s, est remaining 111.4s, peak mem 10185MB, user 2405.0s, sys 23.2s, output queue size 1478
progress 50% @chr10:34269657, elapsed 101.7s, est remaining 101.7s, peak mem 10457MB, user 2691.7s, sys 25.6s, output queue size 105
progress 55% @chr11:48975498, elapsed 110.6s, est remaining 90.5s, peak mem 10457MB, user 2926.0s, sys 27.1s, output queue size 15
progress 60% @chr12:25052235, elapsed 122.7s, est remaining 81.8s, peak mem 10457MB, user 3251.9s, sys 28.9s, output queue size 755
progress 65% @chr13:48706818, elapsed 133.0s, est remaining 71.6s, peak mem 10545MB, user 3526.9s, sys 30.5s, output queue size 567
progress 70% @chr15:42751974, elapsed 142.8s, est remaining 61.2s, peak mem 10570MB, user 3783.8s, sys 32.4s, output queue size 461
progress 75% @chr16:30967501, elapsed 154.6s, est remaining 51.5s, peak mem 10570MB, user 4107.8s, sys 34.3s, output queue size 28
progress 80% @chr17:42687720, elapsed 167.3s, est remaining 41.8s, peak mem 10570MB, user 4458.9s, sys 36.6s, output queue size 698
progress 85% @chr19:5739326, elapsed 179.6s, est remaining 31.7s, peak mem 10570MB, user 4795.1s, sys 38.5s, output queue size 405
progress 90% @chr19:55517224, elapsed 191.0s, est remaining 21.2s, peak mem 10570MB, user 5104.9s, sys 40.3s, output queue size 125
progress 95% @chr22:36490008, elapsed 202.3s, est remaining 10.6s, peak mem 10702MB, user 5410.4s, sys 41.8s, output queue size 29
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 210.7s, est remaining 0.0s, peak mem 10702MB, user 5629.4s, sys 43.1s, output queue size 1
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: 68397013038
reads: 1261745363
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2804.723 user 35.827 sys 2925.268 real
done: 1 calls 0.394 user 0.288 sys 0.683 real
execute: 1 calls 0.005 user 0.001 sys 210.657 real
fetch_reads: 208647 calls 227.139 user 0.533 sys 232.498 real
fetch_ref: 207478 calls 1.147 user 1.016 sys 2.109 real
fetch_vcf: 207478 calls 82.002 user 2.124 sys 86.655 real
idle: 100 calls 0.193 user 0.000 sys 32.238 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 514640 calls 3097.590 user 2.200 sys 3156.911 real
overall: 11222532096 mem 6393.226 user 44.420 sys 212.320 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