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/94/fb16d83703cabc84e7cd51a2a9af08/1136_3MV-T1-TDNA-1_A23MHWWLT4_1.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/05/e2e83afb507756f754151f89f0eaaf/.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/94/fb16d83703cabc84e7cd51a2a9af08/1136_3MV-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/e2e83afb507756f754151f89f0eaaf/.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 1136_3MV-T1-TDNA-1_A23MHWWLT4_1.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 1136_3MV-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:117143588, elapsed 8.2s, est remaining 156.2s, peak mem 5042MB, user 217.2s, sys 4.8s, output queue size 193
progress 10% @chr2:21028327, elapsed 16.6s, est remaining 149.0s, peak mem 6265MB, user 440.3s, sys 7.8s, output queue size 650
progress 15% @chr2:185788643, elapsed 24.6s, est remaining 139.2s, peak mem 6882MB, user 652.6s, sys 9.6s, output queue size 291
progress 20% @chr3:98469577, elapsed 32.8s, est remaining 131.2s, peak mem 6987MB, user 874.8s, sys 11.2s, output queue size 433
progress 25% @chr4:88463855, elapsed 39.6s, est remaining 118.7s, peak mem 6987MB, user 1051.8s, sys 12.7s, output queue size 89
progress 30% @chr5:147395559, elapsed 45.4s, est remaining 105.8s, peak mem 6987MB, user 1201.0s, sys 13.9s, output queue size 209
progress 35% @chr6:131700469, elapsed 56.7s, est remaining 105.2s, peak mem 7682MB, user 1508.7s, sys 16.1s, output queue size 642
progress 40% @chr7:116769636, elapsed 66.6s, est remaining 99.9s, peak mem 8187MB, user 1770.6s, sys 18.0s, output queue size 1463
progress 45% @chr9:2639859, elapsed 77.0s, est remaining 94.1s, peak mem 9609MB, user 2047.6s, sys 19.8s, output queue size 1478
progress 50% @chr10:35054434, elapsed 86.7s, est remaining 86.7s, peak mem 14408MB, user 2263.8s, sys 21.5s, output queue size 11474
progress 55% @chr11:49053714, elapsed 96.4s, est remaining 78.8s, peak mem 21445MB, user 2538.1s, sys 23.9s, output queue size 21868
progress 60% @chr12:11752419, elapsed 107.6s, est remaining 71.8s, peak mem 21604MB, user 2877.1s, sys 31.0s, output queue size 784
progress 65% @chr13:49488290, elapsed 115.3s, est remaining 62.1s, peak mem 21604MB, user 3085.3s, sys 32.4s, output queue size 555
progress 70% @chr15:42736302, elapsed 122.6s, est remaining 52.5s, peak mem 21604MB, user 3280.2s, sys 33.6s, output queue size 456
progress 75% @chr16:30766741, elapsed 132.2s, est remaining 44.1s, peak mem 21604MB, user 3546.7s, sys 35.0s, output queue size 34
progress 80% @chr17:42688462, elapsed 144.4s, est remaining 36.1s, peak mem 21604MB, user 3886.5s, sys 37.1s, output queue size 705
progress 85% @chr19:5696054, elapsed 152.3s, est remaining 26.9s, peak mem 21604MB, user 4099.7s, sys 38.4s, output queue size 403
progress 90% @chr19:55481201, elapsed 161.1s, est remaining 17.9s, peak mem 21604MB, user 4341.5s, sys 40.0s, output queue size 90
progress 95% @chr22:36504098, elapsed 171.8s, est remaining 9.0s, peak mem 21683MB, user 4634.8s, sys 42.0s, output queue size 25
progress 100% @chr6_GL000251v2_alt:3946951, elapsed 181.8s, est remaining 0.0s, peak mem 21815MB, user 4904.8s, sys 43.7s, output queue size 6
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: 66368244287
reads: 1256320583
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2580.258 user 36.493 sys 2706.787 real
done: 1 calls 0.357 user 0.350 sys 0.714 real
execute: 1 calls 0.013 user 0.000 sys 181.845 real
fetch_reads: 208647 calls 213.353 user 0.625 sys 218.333 real
fetch_ref: 207096 calls 0.999 user 0.792 sys 2.098 real
fetch_vcf: 207096 calls 81.601 user 2.150 sys 85.522 real
idle: 167 calls 0.387 user 0.000 sys 34.186 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 465684 calls 2431.015 user 2.216 sys 2494.975 real
overall: 22875709440 mem 5496.456 user 45.284 sys 183.737 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