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/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  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/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fc/8760f164f3eb7f9ac92539edadbe66/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a5/5bccf33822723695cc22b7376f2be6/1136_5L2-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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/fc/8760f164f3eb7f9ac92539edadbe66/.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_5L2-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_5L2-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 7.7s, est remaining 146.2s, peak mem 4900MB, user 200.0s, sys 5.1s, output queue size 176
progress 10% @chr2:17780621, elapsed 14.7s, est remaining 132.2s, peak mem 5610MB, user 384.0s, sys 7.1s, output queue size 651
progress 15% @chr2:190199861, elapsed 23.5s, est remaining 132.9s, peak mem 6358MB, user 616.7s, sys 8.9s, output queue size 295
progress 20% @chr3:98791841, elapsed 32.0s, est remaining 128.0s, peak mem 6722MB, user 842.3s, sys 11.8s, output queue size 423
progress 25% @chr4:88500915, elapsed 38.3s, est remaining 114.9s, peak mem 6722MB, user 1004.7s, sys 13.1s, output queue size 87
progress 30% @chr5:147617911, elapsed 43.9s, est remaining 102.5s, peak mem 6722MB, user 1149.3s, sys 14.2s, output queue size 199
progress 35% @chr6:132401163, elapsed 52.3s, est remaining 97.2s, peak mem 7373MB, user 1370.2s, sys 15.9s, output queue size 638
progress 40% @chr7:128841454, elapsed 61.5s, est remaining 92.3s, peak mem 7874MB, user 1608.1s, sys 17.6s, output queue size 543
progress 45% @chr9:1051614, elapsed 71.0s, est remaining 86.7s, peak mem 8025MB, user 1866.2s, sys 19.2s, output queue size 22
progress 50% @chr10:33330708, elapsed 79.0s, est remaining 79.0s, peak mem 8148MB, user 2078.4s, sys 20.3s, output queue size 106
progress 55% @chr11:48980906, elapsed 85.6s, est remaining 70.0s, peak mem 8148MB, user 2248.0s, sys 21.5s, output queue size 15
progress 60% @chr12:25232559, elapsed 94.6s, est remaining 63.1s, peak mem 8148MB, user 2483.3s, sys 23.3s, output queue size 800
progress 65% @chr13:49541676, elapsed 102.8s, est remaining 55.4s, peak mem 8148MB, user 2706.8s, sys 24.6s, output queue size 564
progress 70% @chr15:42751974, elapsed 110.0s, est remaining 47.2s, peak mem 8148MB, user 2895.9s, sys 25.8s, output queue size 455
progress 75% @chr16:30953185, elapsed 118.2s, est remaining 39.4s, peak mem 8148MB, user 3120.9s, sys 26.9s, output queue size 35
progress 80% @chr17:42315223, elapsed 126.3s, est remaining 31.6s, peak mem 8148MB, user 3338.4s, sys 28.1s, output queue size 695
progress 85% @chr19:5754132, elapsed 133.2s, est remaining 23.5s, peak mem 8148MB, user 3521.3s, sys 29.2s, output queue size 404
progress 90% @chr19:55481201, elapsed 139.9s, est remaining 15.5s, peak mem 8148MB, user 3699.0s, sys 30.2s, output queue size 86
progress 95% @chr22:36320220, elapsed 147.5s, est remaining 7.8s, peak mem 8148MB, user 3900.1s, sys 31.6s, output queue size 26
progress 100% @chr6_GL000254v2_alt:3881705, elapsed 152.3s, est remaining 0.0s, peak mem 8148MB, user 4024.3s, sys 32.3s, output queue size 1
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: 52593107263
reads: 1002659546
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1976.517 user 24.959 sys 2075.378 real
done: 1 calls 0.325 user 0.374 sys 0.704 real
execute: 1 calls 0.010 user 0.000 sys 152.275 real
fetch_reads: 208647 calls 170.475 user 0.301 sys 174.662 real
fetch_ref: 207314 calls 1.153 user 1.026 sys 2.001 real
fetch_vcf: 207314 calls 80.658 user 2.022 sys 85.024 real
idle: 92 calls 0.144 user 0.000 sys 32.332 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 438939 calls 2225.379 user 2.863 sys 2279.182 real
overall: 8544239616 mem 4610.126 user 33.494 sys 153.803 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