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/54/67e80fd959906794093fa1156b5149/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/ca/b758ef17618f14fc6d3195b06dd458/.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/ca/b758ef17618f14fc6d3195b06dd458/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/54/67e80fd959906794093fa1156b5149/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 0.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 4637
progress 10% @chr2:19953834, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2910
progress 15% @chr2:189062865, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 13311
progress 20% @chr3:97947361, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 23795
progress 25% @chr4:88417425, elapsed 0.2s, est remaining 0.7s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 34042
progress 30% @chr5:147383441, elapsed 0.3s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 44081
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 177MB, user 0.0s, sys 0.0s, output queue size 7197
progress 40% @chr7:128754262, elapsed 0.3s, est remaining 0.5s, peak mem 177MB, user 0.0s, sys 0.0s, output queue size 16679
progress 45% @chr9:710804, elapsed 0.4s, est remaining 0.5s, peak mem 297MB, user 0.0s, sys 0.0s, output queue size 26054
progress 50% @chr10:32284698, elapsed 0.4s, est remaining 0.4s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 35986
progress 55% @chr11:48324941, elapsed 0.5s, est remaining 0.4s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 46452
progress 60% @chr12:21906126, elapsed 0.5s, est remaining 0.3s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 56001
progress 65% @chr13:49198362, elapsed 0.5s, est remaining 0.3s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 67053
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.3s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 77103
progress 75% @chr16:30899415, elapsed 0.6s, est remaining 0.2s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 86653
progress 80% @chr17:42543028, elapsed 0.7s, est remaining 0.2s, peak mem 304MB, user 0.0s, sys 0.0s, output queue size 97344
progress 85% @chr19:5650978, elapsed 0.7s, est remaining 0.1s, peak mem 331MB, user 0.0s, sys 0.0s, output queue size 107749
progress 90% @chr19:55731999, elapsed 0.7s, est remaining 0.1s, peak mem 331MB, user 0.0s, sys 0.0s, output queue size 117250
progress 95% @chr22:36504515, elapsed 1.1s, est remaining 0.1s, peak mem 2524MB, user 7.2s, sys 1.8s, output queue size 2424
progress 100% @chr6_GL000251v2_alt:3946951, elapsed 1.2s, est remaining 0.0s, peak mem 2524MB, user 7.2s, sys 1.8s, output queue size 8724
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: 51395352
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.997 user 0.098 sys 2.406 real
done: 1 calls 0.327 user 0.128 sys 0.454 real
execute: 1 calls 0.006 user 0.001 sys 1.184 real
fetch_reads: 208647 calls 0.115 user 0.000 sys 0.171 real
fetch_ref: 2042 calls 0.013 user 0.025 sys 0.025 real
fetch_vcf: 2042 calls 0.819 user 0.037 sys 1.092 real
idle: 92 calls 0.001 user 0.002 sys 31.661 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 5.077 user 1.598 sys 8.049 real
overall: 2647339008 mem 11.099 user 16.272 sys 2.561 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