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/b2/5d2d2a40ebfadd6cf387c9473e6514/Sig_18_tissue.md.bam.bai
  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/b2/5d2d2a40ebfadd6cf387c9473e6514/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d0/708452e2b2a5620be6748c4c9be7f5/.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/d0/708452e2b2a5620be6748c4c9be7f5/.command.run
  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 Sig_18_tissue.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 Sig_18_tissue.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 172MB, user 0.0s, sys 0.0s, output queue size 5187
progress 10% @chr2:17785862, elapsed 0.1s, est remaining 0.7s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 7473
progress 15% @chr2:189043151, elapsed 0.1s, est remaining 0.6s, peak mem 181MB, user 0.0s, sys 0.0s, output queue size 17875
progress 20% @chr3:97871842, elapsed 0.1s, est remaining 0.6s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 28341
progress 25% @chr4:88440148, elapsed 0.2s, est remaining 0.5s, peak mem 192MB, user 0.0s, sys 0.0s, output queue size 9842
progress 30% @chr5:146463551, elapsed 0.2s, est remaining 0.5s, peak mem 210MB, user 0.0s, sys 0.0s, output queue size 19880
progress 35% @chr6:127330809, elapsed 0.3s, est remaining 0.5s, peak mem 210MB, user 0.0s, sys 0.0s, output queue size 29843
progress 40% @chr7:128794348, elapsed 0.3s, est remaining 0.4s, peak mem 219MB, user 0.0s, sys 0.0s, output queue size 39313
progress 45% @chr9:1056216, elapsed 0.3s, est remaining 0.4s, peak mem 373MB, user 0.0s, sys 0.0s, output queue size 48689
progress 50% @chr10:32583034, elapsed 0.4s, est remaining 0.4s, peak mem 421MB, user 0.0s, sys 0.0s, output queue size 58628
progress 55% @chr11:48245104, elapsed 0.4s, est remaining 0.3s, peak mem 456MB, user 0.0s, sys 0.0s, output queue size 69092
progress 60% @chr12:22469709, elapsed 0.4s, est remaining 0.3s, peak mem 459MB, user 0.0s, sys 0.0s, output queue size 78675
progress 65% @chr13:49191015, elapsed 0.5s, est remaining 0.2s, peak mem 489MB, user 0.0s, sys 0.0s, output queue size 89691
progress 70% @chr15:42717977, elapsed 0.5s, est remaining 0.2s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 99729
progress 75% @chr16:30942375, elapsed 0.5s, est remaining 0.2s, peak mem 517MB, user 0.0s, sys 0.1s, output queue size 6238
progress 80% @chr17:42514289, elapsed 0.6s, est remaining 0.1s, peak mem 526MB, user 0.0s, sys 0.1s, output queue size 16933
progress 85% @chr19:5622530, elapsed 0.6s, est remaining 0.1s, peak mem 526MB, user 0.0s, sys 0.1s, output queue size 27340
progress 90% @chr19:55694726, elapsed 0.6s, est remaining 0.1s, peak mem 535MB, user 0.0s, sys 0.1s, output queue size 36832
progress 95% @chr22:36930337, elapsed 1.0s, est remaining 0.1s, peak mem 2532MB, user 7.0s, sys 1.7s, output queue size 2841
progress 100% @chrY:57191798, elapsed 1.0s, est remaining 0.0s, peak mem 2532MB, user 7.1s, sys 1.7s, output queue size 9169
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 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 50044649
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.788 user 0.126 sys 2.020 real
done: 1 calls 0.278 user 0.080 sys 0.362 real
execute: 1 calls 0.008 user 0.001 sys 1.048 real
fetch_reads: 208647 calls 0.068 user 0.000 sys 0.148 real
fetch_ref: 2079 calls 0.000 user 0.004 sys 0.018 real
fetch_vcf: 2079 calls 0.740 user 0.020 sys 0.927 real
idle: 92 calls 0.002 user 0.001 sys 31.601 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 5.546 user 1.523 sys 7.859 real
overall: 2655416320 mem 10.734 user 13.143 sys 2.419 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