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/56/13741b9a5c47905c2325e589b6cf85/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/70/0b29acedfeb470aac125a95a0e0fb7/.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/70/0b29acedfeb470aac125a95a0e0fb7/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13741b9a5c47905c2325e589b6cf85/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 162MB, user 0.0s, sys 0.0s, output queue size 314
progress 10% @chr2:20003161, elapsed 0.1s, est remaining 0.7s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 1698
progress 15% @chr2:189054159, elapsed 0.1s, est remaining 0.6s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 12082
progress 20% @chr3:97871842, elapsed 0.1s, est remaining 0.6s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 22549
progress 25% @chr4:88462135, elapsed 0.2s, est remaining 0.5s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 5805
progress 30% @chr5:147375090, elapsed 0.2s, est remaining 0.5s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 15843
progress 35% @chr6:127135950, elapsed 0.2s, est remaining 0.4s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 25792
progress 40% @chr7:128774498, elapsed 0.3s, est remaining 0.4s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 35278
progress 45% @chr9:1975291, elapsed 0.3s, est remaining 0.3s, peak mem 265MB, user 0.0s, sys 0.0s, output queue size 44649
progress 50% @chr10:32022020, elapsed 0.3s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 54594
progress 55% @chr11:48488793, elapsed 0.3s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 65051
progress 60% @chr12:21475669, elapsed 0.4s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 74603
progress 65% @chr13:49267490, elapsed 0.4s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 85654
progress 70% @chr15:42665786, elapsed 0.4s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 95684
progress 75% @chr16:30930073, elapsed 0.4s, est remaining 0.1s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 105250
progress 80% @chr17:42553124, elapsed 0.5s, est remaining 0.1s, peak mem 306MB, user 0.0s, sys 0.0s, output queue size 3687
progress 85% @chr19:5661518, elapsed 0.5s, est remaining 0.1s, peak mem 333MB, user 0.0s, sys 0.0s, output queue size 14104
progress 90% @chr19:55678527, elapsed 0.5s, est remaining 0.1s, peak mem 343MB, user 0.0s, sys 0.1s, output queue size 23598
progress 95% @chr22:36501241, elapsed 0.9s, est remaining 0.0s, peak mem 2520MB, user 7.4s, sys 1.7s, output queue size 285
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 0.9s, est remaining 0.0s, peak mem 2520MB, user 7.4s, sys 1.7s, output queue size 9912
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000c06f2
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: INTEL(R) XEON(R) PLATINUM 8559C
threads: 31 max 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 51395363
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2.122 user 0.108 sys 2.446 real
done: 1 calls 0.323 user 0.088 sys 0.415 real
execute: 1 calls 0.002 user 0.010 sys 0.923 real
fetch_reads: 208647 calls 0.090 user 0.000 sys 0.160 real
fetch_ref: 2042 calls 0.011 user 0.013 sys 0.014 real
fetch_vcf: 2042 calls 0.950 user 0.062 sys 1.089 real
idle: 92 calls 0.002 user 0.000 sys 31.644 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 4.964 user 1.557 sys 6.978 real
overall: 2642788352 mem 11.111 user 5.572 sys 2.331 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