Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4b/8a67a4930c75ff0573fec03e4ea2c8/1136_4Z5-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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/7c/6800a314c78ffd24bdcdc3c069369f/.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/7c/6800a314c78ffd24bdcdc3c069369f/.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_4Z5-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_4Z5-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 6.4s, est remaining 120.7s, peak mem 4660MB, user 173.0s, sys 4.1s, output queue size 173
progress 10% @chr2:21029898, elapsed 12.8s, est remaining 115.3s, peak mem 5606MB, user 350.0s, sys 6.4s, output queue size 660
progress 15% @chr2:190534559, elapsed 22.3s, est remaining 126.5s, peak mem 8926MB, user 610.8s, sys 10.1s, output queue size 4167
progress 20% @chr3:98732864, elapsed 29.2s, est remaining 116.9s, peak mem 8926MB, user 806.7s, sys 11.6s, output queue size 424
progress 25% @chr4:88462135, elapsed 34.4s, est remaining 103.2s, peak mem 8926MB, user 948.6s, sys 12.6s, output queue size 88
progress 30% @chr5:147399082, elapsed 39.0s, est remaining 91.1s, peak mem 8926MB, user 1074.2s, sys 13.4s, output queue size 208
progress 35% @chr6:131700469, elapsed 51.2s, est remaining 95.1s, peak mem 10716MB, user 1422.3s, sys 16.9s, output queue size 638
progress 40% @chr7:130279463, elapsed 63.4s, est remaining 95.2s, peak mem 25580MB, user 1684.3s, sys 20.8s, output queue size 4414
progress 45% @chr9:5064883, elapsed 76.0s, est remaining 92.9s, peak mem 44462MB, user 2012.7s, sys 37.1s, output queue size 13683
progress 50% @chr10:42592613, elapsed 84.5s, est remaining 84.5s, peak mem 49801MB, user 2209.5s, sys 38.4s, output queue size 23675
progress 55% @chr11:55811467, elapsed 92.2s, est remaining 75.5s, peak mem 54984MB, user 2448.5s, sys 46.3s, output queue size 33988
progress 60% @chr12:26230711, elapsed 100.0s, est remaining 66.6s, peak mem 56852MB, user 2718.3s, sys 55.7s, output queue size 43644
progress 65% @chr13:51110796, elapsed 107.8s, est remaining 58.0s, peak mem 57512MB, user 2928.9s, sys 57.2s, output queue size 54632
progress 70% @chr15:41765986, elapsed 116.2s, est remaining 49.8s, peak mem 59121MB, user 3154.5s, sys 58.8s, output queue size 64739
progress 75% @chr16:31085964, elapsed 123.2s, est remaining 41.1s, peak mem 60354MB, user 3342.5s, sys 60.1s, output queue size 74189
progress 80% @chr17:42794772, elapsed 131.5s, est remaining 32.9s, peak mem 60366MB, user 3568.6s, sys 61.3s, output queue size 84960
progress 85% @chr19:5843754, elapsed 138.5s, est remaining 24.4s, peak mem 60366MB, user 3757.3s, sys 62.7s, output queue size 95343
progress 90% @chr19:56032611, elapsed 146.7s, est remaining 16.3s, peak mem 60366MB, user 3981.3s, sys 64.2s, output queue size 104781
progress 95% @chr22:37182188, elapsed 154.3s, est remaining 8.1s, peak mem 60366MB, user 4184.5s, sys 65.5s, output queue size 114579
progress 100% @chr7:55176897, elapsed 184.9s, est remaining 0.0s, peak mem 60521MB, user 4434.2s, sys 74.2s, output queue size 124110
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: 71921241447
reads: 1527741288
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2535.131 user 64.632 sys 2701.315 real
done: 1 calls 0.375 user 0.295 sys 0.678 real
execute: 1 calls 0.001 user 0.010 sys 186.564 real
fetch_reads: 208647 calls 262.432 user 2.119 sys 273.553 real
fetch_ref: 206946 calls 1.122 user 0.966 sys 2.262 real
fetch_vcf: 206946 calls 79.488 user 2.006 sys 85.720 real
idle: 1400 calls 1.918 user 0.026 sys 851.772 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 431471 calls 1708.309 user 2.420 sys 1772.140 real
overall: 63460880384 mem 4809.389 user 76.681 sys 189.608 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