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/5d/9bc2477a071584c0387d1c6464c441/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/f8/cc3b084f0343a81efbf9c980a3334f/.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/f8/cc3b084f0343a81efbf9c980a3334f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5d/9bc2477a071584c0387d1c6464c441/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 98
progress 10% @chr2:20005744, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 4866
progress 15% @chr2:189051320, elapsed 0.1s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 3727
progress 20% @chr3:97933694, elapsed 0.1s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 14215
progress 25% @chr4:88460095, elapsed 0.2s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 24459
progress 30% @chr5:146514854, elapsed 0.2s, est remaining 0.5s, peak mem 175MB, user 0.0s, sys 0.0s, output queue size 1039
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 175MB, user 0.0s, sys 0.0s, output queue size 10992
progress 40% @chr7:128772540, elapsed 0.3s, est remaining 0.4s, peak mem 175MB, user 0.0s, sys 0.0s, output queue size 20472
progress 45% @chr9:2047229, elapsed 0.3s, est remaining 0.4s, peak mem 294MB, user 0.0s, sys 0.0s, output queue size 29847
progress 50% @chr10:32287098, elapsed 0.4s, est remaining 0.4s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 39780
progress 55% @chr11:48216810, elapsed 0.4s, est remaining 0.3s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 50252
progress 60% @chr12:21910826, elapsed 0.4s, est remaining 0.3s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 59795
progress 65% @chr13:49220338, elapsed 0.5s, est remaining 0.3s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 70846
progress 70% @chr15:42872611, elapsed 0.5s, est remaining 0.2s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 80944
progress 75% @chr16:30902078, elapsed 0.6s, est remaining 0.2s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 90448
progress 80% @chr17:42540950, elapsed 0.6s, est remaining 0.2s, peak mem 303MB, user 0.0s, sys 0.1s, output queue size 101140
progress 85% @chr19:5611120, elapsed 0.6s, est remaining 0.1s, peak mem 339MB, user 0.0s, sys 0.1s, output queue size 111547
progress 90% @chr19:55694726, elapsed 0.7s, est remaining 0.1s, peak mem 339MB, user 0.0s, sys 0.1s, output queue size 121043
progress 95% @chr22:37018138, elapsed 1.1s, est remaining 0.1s, peak mem 2514MB, user 5.9s, sys 2.9s, output queue size 3230
progress 100% @chr6_GL000251v2_alt:3939000, elapsed 1.1s, est remaining 0.0s, peak mem 2514MB, user 6.0s, sys 2.9s, output queue size 6777
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: 51394930
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.762 user 0.114 sys 2.220 real
done: 1 calls 0.314 user 0.120 sys 0.436 real
execute: 1 calls 0.009 user 0.000 sys 1.112 real
fetch_reads: 208647 calls 0.044 user 0.000 sys 0.161 real
fetch_ref: 2042 calls 0.020 user 0.020 sys 0.023 real
fetch_vcf: 2042 calls 0.813 user 0.042 sys 0.967 real
idle: 90 calls 0.002 user 0.002 sys 31.571 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 4.101 user 2.664 sys 7.257 real
overall: 2636349440 mem 9.620 user 16.863 sys 2.486 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