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/e8/a21cfb3f7d608a4f5c8a7d1506352c/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/4e/a74b287cf812db599fb85d0d19d6b7/.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/4e/a74b287cf812db599fb85d0d19d6b7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/a21cfb3f7d608a4f5c8a7d1506352c/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 0.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 125
progress 10% @chr2:17787902, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 125
progress 15% @chr2:189054159, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 355
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 218
progress 25% @chr4:88459347, elapsed 0.2s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 1538
progress 30% @chr5:147401540, elapsed 0.2s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 7006
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 5999
progress 40% @chr7:128810139, elapsed 0.3s, est remaining 0.5s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 15441
progress 45% @chr9:710804, elapsed 0.4s, est remaining 0.4s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 7530
progress 50% @chr10:32689053, elapsed 0.4s, est remaining 0.4s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 17481
progress 55% @chr11:48306223, elapsed 0.5s, est remaining 0.4s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 27937
progress 60% @chr12:21916937, elapsed 0.5s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 37487
progress 65% @chr13:49174435, elapsed 0.5s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 48536
progress 70% @chr15:42682104, elapsed 0.6s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 58571
progress 75% @chr16:30930073, elapsed 0.6s, est remaining 0.2s, peak mem 303MB, user 0.0s, sys 0.0s, output queue size 4269
progress 80% @chr17:42543028, elapsed 0.7s, est remaining 0.2s, peak mem 303MB, user 0.0s, sys 0.0s, output queue size 14958
progress 85% @chr19:5611120, elapsed 0.7s, est remaining 0.1s, peak mem 339MB, user 0.0s, sys 0.0s, output queue size 25366
progress 90% @chr19:55592450, elapsed 0.8s, est remaining 0.1s, peak mem 339MB, user 0.0s, sys 0.0s, output queue size 34877
progress 95% @chr22:37011027, elapsed 1.1s, est remaining 0.1s, peak mem 2512MB, user 5.7s, sys 2.1s, output queue size 3227
progress 100% @chrY:57189969, elapsed 1.1s, est remaining 0.0s, peak mem 2512MB, user 5.9s, sys 2.1s, output queue size 1259
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: 51394901
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.700 user 0.102 sys 2.164 real
done: 1 calls 0.299 user 0.080 sys 0.384 real
execute: 1 calls 0.013 user 0.001 sys 1.143 real
fetch_reads: 208647 calls 0.095 user 0.003 sys 0.155 real
fetch_ref: 2042 calls 0.011 user 0.016 sys 0.026 real
fetch_vcf: 2042 calls 0.847 user 0.028 sys 0.948 real
idle: 92 calls 0.003 user 0.001 sys 31.584 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 3.827 user 1.955 sys 6.287 real
overall: 2634813440 mem 9.689 user 10.852 sys 2.511 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