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-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/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/81/32d20394dabccc95f5fb57d32d2428/.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/81/32d20394dabccc95f5fb57d32d2428/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/00/6deb667df284430001177d0a9637ad/HCC1395_tumor.md.bam
  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_tumor.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_tumor.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119922603, elapsed 0.0s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 156
progress 10% @chr2:19994299, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2249
progress 15% @chr2:189053895, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 5704
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 16187
progress 25% @chr4:88131061, elapsed 0.2s, est remaining 0.7s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 3255
progress 30% @chr5:147397666, elapsed 0.3s, est remaining 0.7s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 13293
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 23252
progress 40% @chr7:128359340, elapsed 0.4s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 32734
progress 45% @chr9:977002, elapsed 0.4s, est remaining 0.5s, peak mem 334MB, user 0.0s, sys 0.1s, output queue size 42087
progress 50% @chr10:32728887, elapsed 0.5s, est remaining 0.5s, peak mem 334MB, user 0.0s, sys 0.1s, output queue size 52051
progress 55% @chr11:48324941, elapsed 0.5s, est remaining 0.4s, peak mem 334MB, user 0.0s, sys 0.1s, output queue size 62500
progress 60% @chr12:22062281, elapsed 0.6s, est remaining 0.4s, peak mem 343MB, user 0.0s, sys 0.1s, output queue size 3410
progress 65% @chr13:49131137, elapsed 0.6s, est remaining 0.3s, peak mem 346MB, user 0.0s, sys 0.1s, output queue size 14464
progress 70% @chr15:42684116, elapsed 0.7s, est remaining 0.3s, peak mem 355MB, user 0.0s, sys 0.1s, output queue size 24500
progress 75% @chr16:30781718, elapsed 0.7s, est remaining 0.2s, peak mem 355MB, user 0.0s, sys 0.1s, output queue size 34062
progress 80% @chr17:42494334, elapsed 0.8s, est remaining 0.2s, peak mem 355MB, user 0.0s, sys 0.1s, output queue size 44744
progress 85% @chr19:5680055, elapsed 0.8s, est remaining 0.1s, peak mem 397MB, user 0.0s, sys 0.1s, output queue size 55165
progress 90% @chr19:55688870, elapsed 0.8s, est remaining 0.1s, peak mem 400MB, user 0.0s, sys 0.1s, output queue size 64657
progress 95% @chr22:36935302, elapsed 1.3s, est remaining 0.1s, peak mem 2473MB, user 8.0s, sys 2.3s, output queue size 3227
progress 100% @chr6_GL000254v2_alt:3877871, elapsed 1.3s, est remaining 0.0s, peak mem 2473MB, user 8.1s, sys 2.3s, output queue size 6144
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 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 50813895
reads: 1001320
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2.141 user 0.124 sys 2.570 real
done: 1 calls 0.312 user 0.098 sys 0.411 real
execute: 1 calls 0.000 user 0.010 sys 1.305 real
fetch_reads: 208647 calls 0.166 user 0.001 sys 0.196 real
fetch_ref: 2048 calls 0.007 user 0.017 sys 0.028 real
fetch_vcf: 2048 calls 0.914 user 0.021 sys 1.077 real
idle: 90 calls 0.003 user 0.001 sys 31.682 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2195 calls 5.660 user 2.134 sys 8.431 real
overall: 2594058240 mem 12.544 user 13.154 sys 2.700 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