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/b3/57a16f0cfbc17f3f3dcbee22c14121/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/63/33a462347e84f707d890a9e2d47601/.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/63/33a462347e84f707d890a9e2d47601/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/57a16f0cfbc17f3f3dcbee22c14121/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% @chr1:119893964, elapsed 0.0s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 111
progress 10% @chr2:19945786, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2408
progress 15% @chr2:189039272, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 9115
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 9442
progress 25% @chr4:88439874, elapsed 0.2s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 19691
progress 30% @chr5:147401540, elapsed 0.2s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 29730
progress 35% @chr6:127444109, elapsed 0.3s, est remaining 0.5s, peak mem 175MB, user 0.0s, sys 0.0s, output queue size 5318
progress 40% @chr7:128476766, elapsed 0.3s, est remaining 0.5s, peak mem 175MB, user 0.0s, sys 0.0s, output queue size 14806
progress 45% @chr9:2039466, elapsed 0.3s, est remaining 0.4s, peak mem 285MB, user 0.0s, sys 0.0s, output queue size 24182
progress 50% @chr10:32451643, elapsed 0.4s, est remaining 0.4s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 34113
progress 55% @chr11:48365485, elapsed 0.4s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 44578
progress 60% @chr12:21916937, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 54125
progress 65% @chr13:49259346, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 65182
progress 70% @chr15:42684116, elapsed 0.5s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 75218
progress 75% @chr16:30893212, elapsed 0.6s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 84777
progress 80% @chr17:42554669, elapsed 0.6s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 95472
progress 85% @chr19:5653115, elapsed 0.7s, est remaining 0.1s, peak mem 337MB, user 0.0s, sys 0.1s, output queue size 105881
progress 90% @chr19:55692686, elapsed 0.7s, est remaining 0.1s, peak mem 339MB, user 0.0s, sys 0.1s, output queue size 115378
progress 95% @chr22:36937342, elapsed 1.0s, est remaining 0.1s, peak mem 2526MB, user 5.4s, sys 2.0s, output queue size 3227
progress 100% @chr6_GL000254v2_alt:3877373, elapsed 1.0s, est remaining 0.0s, peak mem 2526MB, user 5.5s, sys 2.0s, output queue size 2986
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 51394915
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.704 user 0.096 sys 2.033 real
done: 1 calls 0.294 user 0.078 sys 0.380 real
execute: 1 calls 0.011 user 0.000 sys 1.053 real
fetch_reads: 208647 calls 0.101 user 0.001 sys 0.144 real
fetch_ref: 2042 calls 0.001 user 0.008 sys 0.022 real
fetch_vcf: 2042 calls 0.758 user 0.031 sys 0.916 real
idle: 92 calls 0.003 user 0.001 sys 31.655 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 3.513 user 1.867 sys 6.070 real
overall: 2648973312 mem 9.661 user 9.992 sys 2.425 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