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/59/bc5e7b7f2c48b2e51fd97162601462/HCC1395_BL.md.bam
  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/89/97a9b995bd488086812ef83bdc3efc/.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/89/97a9b995bd488086812ef83bdc3efc/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/bc5e7b7f2c48b2e51fd97162601462/HCC1395_BL.md.bam.bai
  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 HCC1395_BL.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 HCC1395_BL.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119919268, elapsed 0.0s, est remaining 0.8s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 4598
progress 10% @chr2:20012409, elapsed 0.1s, est remaining 0.7s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 5908
progress 15% @chr2:189043151, elapsed 0.1s, est remaining 0.7s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 16300
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 2896
progress 25% @chr4:88435725, elapsed 0.2s, est remaining 0.6s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 13163
progress 30% @chr5:147418447, elapsed 0.2s, est remaining 0.6s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 23209
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 33153
progress 40% @chr7:128809450, elapsed 0.3s, est remaining 0.5s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 42634
progress 45% @chr9:2039466, elapsed 0.4s, est remaining 0.4s, peak mem 284MB, user 0.0s, sys 0.0s, output queue size 52005
progress 50% @chr10:32033845, elapsed 0.4s, est remaining 0.4s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 61945
progress 55% @chr11:48365485, elapsed 0.4s, est remaining 0.4s, peak mem 301MB, user 0.0s, sys 0.0s, output queue size 72403
progress 60% @chr12:21916937, elapsed 0.5s, est remaining 0.3s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 8487
progress 65% @chr13:49222040, elapsed 0.5s, est remaining 0.3s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 19541
progress 70% @chr15:42544083, elapsed 0.6s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 29576
progress 75% @chr16:30930073, elapsed 0.6s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 39139
progress 80% @chr17:42564709, elapsed 0.6s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 49832
progress 85% @chr19:5687503, elapsed 0.7s, est remaining 0.1s, peak mem 340MB, user 0.0s, sys 0.0s, output queue size 60245
progress 90% @chr19:55731999, elapsed 0.7s, est remaining 0.1s, peak mem 343MB, user 0.0s, sys 0.0s, output queue size 69734
progress 95% @chr22:36937342, elapsed 1.1s, est remaining 0.1s, peak mem 2522MB, user 7.9s, sys 1.9s, output queue size 3223
progress 100% @chrY:57084632, elapsed 1.2s, est remaining 0.0s, peak mem 2522MB, user 8.0s, sys 1.9s, output queue size 1875
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: 1f8bfbff fffab20b
  extended: f1bf07ab 1a407f7e
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) Platinum 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 51395360
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2.283 user 0.075 sys 2.679 real
done: 1 calls 0.304 user 0.139 sys 0.442 real
execute: 1 calls 0.003 user 0.010 sys 1.160 real
fetch_reads: 208647 calls 0.086 user 0.000 sys 0.180 real
fetch_ref: 2042 calls 0.036 user 0.005 sys 0.029 real
fetch_vcf: 2042 calls 1.058 user 0.043 sys 1.170 real
idle: 92 calls 0.002 user 0.001 sys 31.789 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 5.382 user 1.816 sys 7.784 real
overall: 2645147648 mem 11.470 user 6.134 sys 2.614 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