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/71/81816b54ab7484624d9fee8b6881d3/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/ee/aee85eec2e1da65108f0fe28adc566/.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/ee/aee85eec2e1da65108f0fe28adc566/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/71/81816b54ab7484624d9fee8b6881d3/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% @chr1:119922603, elapsed 0.1s, est remaining 1.0s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 4103
progress 10% @chr2:20005744, elapsed 0.1s, est remaining 0.8s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 7841
progress 15% @chr2:189052911, elapsed 0.1s, est remaining 0.8s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 18237
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 28720
progress 25% @chr4:88439874, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2704
progress 30% @chr5:147397666, elapsed 0.3s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 12752
progress 35% @chr6:127144950, elapsed 0.3s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 22691
progress 40% @chr7:128806688, elapsed 0.4s, est remaining 0.5s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 32181
progress 45% @chr9:846960, elapsed 0.4s, est remaining 0.5s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 41537
progress 50% @chr10:32346763, elapsed 0.4s, est remaining 0.4s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 51484
progress 55% @chr11:48263861, elapsed 0.5s, est remaining 0.4s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 61953
progress 60% @chr12:21872625, elapsed 0.5s, est remaining 0.4s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 71501
progress 65% @chr13:49220338, elapsed 0.6s, est remaining 0.3s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 82549
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.3s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 92613
progress 75% @chr16:30902078, elapsed 0.7s, est remaining 0.2s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 102154
progress 80% @chr17:42543028, elapsed 0.7s, est remaining 0.2s, peak mem 289MB, user 0.0s, sys 0.1s, output queue size 112840
progress 85% @chr19:5668162, elapsed 0.8s, est remaining 0.1s, peak mem 313MB, user 0.0s, sys 0.1s, output queue size 9359
progress 90% @chr19:55695148, elapsed 0.8s, est remaining 0.1s, peak mem 328MB, user 0.0s, sys 0.1s, output queue size 18851
progress 95% @chr22:36935567, elapsed 1.2s, est remaining 0.1s, peak mem 2494MB, user 6.2s, sys 2.5s, output queue size 3229
progress 100% @chrY:57087017, elapsed 1.2s, est remaining 0.0s, peak mem 2494MB, user 6.3s, sys 2.5s, output queue size 25
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 51395350
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.840 user 0.217 sys 2.348 real
done: 1 calls 0.207 user 0.147 sys 0.362 real
execute: 1 calls 0.005 user 0.002 sys 1.244 real
fetch_reads: 208647 calls 0.094 user 0.003 sys 0.175 real
fetch_ref: 2042 calls 0.003 user 0.013 sys 0.028 real
fetch_vcf: 2042 calls 0.820 user 0.078 sys 1.019 real
idle: 92 calls 0.001 user 0.003 sys 31.702 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 4.286 user 2.170 sys 7.029 real
overall: 2615463936 mem 9.293 user 19.423 sys 2.626 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