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/f2/e9c80fed45cad6c15f82ff1df9ecf8/1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.bam
  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-rnd-pltf-dev-nextflow-scratch-01/work/f2/e9c80fed45cad6c15f82ff1df9ecf8/1136_3WJ-T1-TDNA-1_A23MHWWLT4_1.md.bam.bai
  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/b5/be6efe9f2a94789f8905d7c903d68f/.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/b5/be6efe9f2a94789f8905d7c903d68f/.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_3WJ-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_3WJ-T1-TDNA-1_A23MHWWLT4_1.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:120048858, elapsed 5.3s, est remaining 100.9s, peak mem 4098MB, user 140.0s, sys 4.4s, output queue size 171
progress 10% @chr2:21014448, elapsed 10.0s, est remaining 90.1s, peak mem 4640MB, user 265.2s, sys 5.9s, output queue size 651
progress 15% @chr2:190199861, elapsed 15.0s, est remaining 84.8s, peak mem 5161MB, user 397.5s, sys 7.2s, output queue size 289
progress 20% @chr3:98532034, elapsed 20.3s, est remaining 81.2s, peak mem 5161MB, user 542.0s, sys 8.2s, output queue size 420
progress 25% @chr4:87661962, elapsed 24.5s, est remaining 73.6s, peak mem 5161MB, user 653.7s, sys 9.0s, output queue size 95
progress 30% @chr5:147639632, elapsed 28.3s, est remaining 66.0s, peak mem 5161MB, user 752.8s, sys 9.7s, output queue size 207
progress 35% @chr6:127143030, elapsed 34.0s, est remaining 63.2s, peak mem 5170MB, user 906.3s, sys 10.9s, output queue size 631
progress 40% @chr7:116769636, elapsed 39.2s, est remaining 58.7s, peak mem 5398MB, user 1041.9s, sys 11.9s, output queue size 533
progress 45% @chr9:2032952, elapsed 44.5s, est remaining 54.4s, peak mem 5657MB, user 1187.8s, sys 13.0s, output queue size 19
progress 50% @chr10:32925871, elapsed 49.7s, est remaining 49.7s, peak mem 5666MB, user 1326.8s, sys 14.2s, output queue size 98
progress 55% @chr11:48144675, elapsed 54.4s, est remaining 44.5s, peak mem 5698MB, user 1452.2s, sys 15.0s, output queue size 20
progress 60% @chr12:25052910, elapsed 59.7s, est remaining 39.8s, peak mem 5698MB, user 1593.4s, sys 15.9s, output queue size 754
progress 65% @chr13:49524085, elapsed 64.8s, est remaining 34.9s, peak mem 5710MB, user 1733.7s, sys 16.7s, output queue size 570
progress 70% @chr15:42736302, elapsed 69.5s, est remaining 29.8s, peak mem 5710MB, user 1860.8s, sys 17.6s, output queue size 456
progress 75% @chr16:30953185, elapsed 74.9s, est remaining 25.0s, peak mem 5710MB, user 2010.1s, sys 18.5s, output queue size 37
progress 80% @chr17:42676402, elapsed 81.2s, est remaining 20.3s, peak mem 5710MB, user 2182.6s, sys 19.7s, output queue size 706
progress 85% @chr19:5763215, elapsed 86.3s, est remaining 15.2s, peak mem 5710MB, user 2321.0s, sys 20.7s, output queue size 408
progress 90% @chr19:55577951, elapsed 91.5s, est remaining 10.2s, peak mem 5710MB, user 2463.6s, sys 21.5s, output queue size 73
progress 95% @chr22:36762904, elapsed 97.1s, est remaining 5.1s, peak mem 5922MB, user 2614.4s, sys 22.4s, output queue size 26
progress 100% @chrY:25622443, elapsed 100.3s, est remaining 0.0s, peak mem 5955MB, user 2701.9s, sys 23.2s, output queue size 31
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: 40063100595
reads: 753549713
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1388.541 user 16.009 sys 1466.292 real
done: 1 calls 0.441 user 0.259 sys 0.702 real
execute: 1 calls 0.004 user 0.010 sys 100.312 real
fetch_reads: 208647 calls 100.133 user 0.216 sys 104.862 real
fetch_ref: 207089 calls 0.994 user 0.860 sys 1.928 real
fetch_vcf: 207089 calls 79.854 user 2.089 sys 84.498 real
idle: 92 calls 0.128 user 0.000 sys 32.232 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 336375 calls 1317.109 user 3.027 sys 1369.170 real
overall: 6245003264 mem 3020.788 user 24.288 sys 101.806 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