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/8a/65c3a895f3cf1f1d8a74bf73c8312b/659_cVw-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/da18e74345445a1ec45f3418d4fda9/.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/8a/65c3a895f3cf1f1d8a74bf73c8312b/659_cVw-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e6/da18e74345445a1ec45f3418d4fda9/.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 659_cVw-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 659_cVw-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:114705781, elapsed 9.7s, est remaining 185.2s, peak mem 6003MB, user 261.2s, sys 6.5s, output queue size 407
progress 10% @chr2:21029639, elapsed 19.1s, est remaining 171.6s, peak mem 7257MB, user 517.5s, sys 9.8s, output queue size 647
progress 15% @chr2:189666133, elapsed 31.4s, est remaining 178.1s, peak mem 8241MB, user 863.3s, sys 12.8s, output queue size 453
progress 20% @chr3:100283607, elapsed 43.0s, est remaining 172.1s, peak mem 9374MB, user 1184.1s, sys 15.6s, output queue size 704
progress 25% @chr4:88504232, elapsed 51.9s, est remaining 155.7s, peak mem 9374MB, user 1428.0s, sys 17.6s, output queue size 540
progress 30% @chr5:147640704, elapsed 59.7s, est remaining 139.3s, peak mem 9424MB, user 1639.4s, sys 19.2s, output queue size 211
progress 35% @chr6:131890341, elapsed 70.5s, est remaining 130.9s, peak mem 9433MB, user 1932.9s, sys 21.1s, output queue size 636
progress 40% @chr7:128844004, elapsed 83.5s, est remaining 125.3s, peak mem 10211MB, user 2294.2s, sys 23.8s, output queue size 541
progress 45% @chr9:916763, elapsed 96.6s, est remaining 118.0s, peak mem 10367MB, user 2663.5s, sys 26.4s, output queue size 28
progress 50% @chr10:33221719, elapsed 107.7s, est remaining 107.7s, peak mem 10461MB, user 2972.7s, sys 28.3s, output queue size 106
progress 55% @chr11:48216810, elapsed 117.2s, est remaining 95.9s, peak mem 10461MB, user 3228.5s, sys 29.8s, output queue size 12
progress 60% @chr12:25011371, elapsed 128.1s, est remaining 85.4s, peak mem 10461MB, user 3529.8s, sys 31.8s, output queue size 753
progress 65% @chr13:49267490, elapsed 138.7s, est remaining 74.7s, peak mem 10461MB, user 3822.1s, sys 33.4s, output queue size 568
progress 70% @chr15:43135512, elapsed 148.8s, est remaining 63.8s, peak mem 10461MB, user 4096.2s, sys 34.7s, output queue size 454
progress 75% @chr16:30953185, elapsed 159.9s, est remaining 53.3s, peak mem 10461MB, user 4407.9s, sys 36.5s, output queue size 35
progress 80% @chr17:42697554, elapsed 171.6s, est remaining 42.9s, peak mem 10461MB, user 4732.2s, sys 38.6s, output queue size 703
progress 85% @chr19:5754132, elapsed 182.0s, est remaining 32.1s, peak mem 10461MB, user 5021.2s, sys 40.2s, output queue size 405
progress 90% @chr19:55517224, elapsed 192.0s, est remaining 21.3s, peak mem 10461MB, user 5294.5s, sys 41.7s, output queue size 57
progress 95% @chr22:36524596, elapsed 202.6s, est remaining 10.7s, peak mem 10461MB, user 5587.7s, sys 43.7s, output queue size 11
progress 100% @chr6_GL000251v2_alt:3939000, elapsed 209.3s, est remaining 0.0s, peak mem 10461MB, user 5764.2s, sys 44.8s, output queue size 7
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: 79716908892
reads: 1583694629
contig: 201779 intervals 37922265 bases
advance: 208647 calls 3031.311 user 36.159 sys 3174.902 real
done: 1 calls 0.398 user 0.298 sys 0.695 real
execute: 1 calls 0.007 user 0.001 sys 209.272 real
fetch_reads: 208647 calls 272.552 user 0.466 sys 280.626 real
fetch_ref: 207354 calls 1.227 user 1.089 sys 2.226 real
fetch_vcf: 207354 calls 81.979 user 1.947 sys 86.242 real
idle: 135 calls 0.251 user 0.000 sys 33.127 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 529924 calls 2722.062 user 3.433 sys 2794.784 real
overall: 10969198592 mem 6331.198 user 46.106 sys 210.888 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