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/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/da/9c5d7ca24e41997875ac913f10d9b5/.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/da/9c5d7ca24e41997875ac913f10d9b5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ef/1b780e82228e825cb40abaea84a098/HCC1395_tumor.md.bam
  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 HCC1395_tumor.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 HCC1395_tumor.table
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
progress 5% @chr1:119893964, elapsed 60.0s, est remaining 1140.6s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 6327
progress 10% @chr2:19989165, elapsed 60.1s, est remaining 540.6s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 4331
progress 15% @chr2:189063172, elapsed 60.1s, est remaining 340.5s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 14729
progress 20% @chr3:97871842, elapsed 60.1s, est remaining 240.5s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 25206
progress 25% @chr4:88459347, elapsed 60.2s, est remaining 180.5s, peak mem 168MB, user 0.0s, sys 0.0s, output queue size 35459
progress 30% @chr5:146701045, elapsed 60.2s, est remaining 140.4s, peak mem 176MB, user 0.0s, sys 0.0s, output queue size 45494
progress 35% @chr6:127812883, elapsed 60.2s, est remaining 111.8s, peak mem 176MB, user 0.0s, sys 0.0s, output queue size 55483
progress 40% @chr7:128811800, elapsed 60.2s, est remaining 90.4s, peak mem 177MB, user 0.0s, sys 0.0s, output queue size 64932
progress 45% @chr9:2015220, elapsed 60.3s, est remaining 73.7s, peak mem 355MB, user 0.0s, sys 0.0s, output queue size 7281
progress 50% @chr10:32456251, elapsed 60.3s, est remaining 60.3s, peak mem 364MB, user 0.0s, sys 0.1s, output queue size 17215
progress 55% @chr11:48306223, elapsed 60.3s, est remaining 49.4s, peak mem 364MB, user 0.0s, sys 0.1s, output queue size 27678
progress 60% @chr12:21910826, elapsed 60.4s, est remaining 40.2s, peak mem 369MB, user 0.0s, sys 0.1s, output queue size 37230
progress 65% @chr13:49198362, elapsed 60.4s, est remaining 32.5s, peak mem 374MB, user 0.0s, sys 0.1s, output queue size 48284
progress 70% @chr15:42718752, elapsed 60.4s, est remaining 25.9s, peak mem 384MB, user 0.0s, sys 0.1s, output queue size 58312
progress 75% @chr16:30759012, elapsed 60.5s, est remaining 20.2s, peak mem 387MB, user 0.0s, sys 0.1s, output queue size 67878
progress 80% @chr17:42562612, elapsed 60.5s, est remaining 15.1s, peak mem 388MB, user 0.0s, sys 0.1s, output queue size 78567
progress 85% @chr19:5609995, elapsed 60.5s, est remaining 10.7s, peak mem 424MB, user 0.0s, sys 0.1s, output queue size 88982
progress 90% @chr19:55731999, elapsed 60.6s, est remaining 6.7s, peak mem 436MB, user 0.0s, sys 0.1s, output queue size 98479
progress 95% @chr22:36518763, elapsed 61.0s, est remaining 3.2s, peak mem 2551MB, user 9.8s, sys 1.6s, output queue size 3226
progress 100% @chr6_GL000251v2_alt:3935152, elapsed 61.0s, est remaining 0.0s, peak mem 2551MB, user 10.0s, sys 1.6s, output queue size 1510
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 64
algo: QualCal
license: sentieon:QualCal=31
input file size: 50813910
reads: 1001320
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2.530 user 0.076 sys 2.785 real
done: 1 calls 0.244 user 0.089 sys 0.336 real
execute: 1 calls 0.001 user 0.008 sys 61.042 real
fetch_reads: 208647 calls 0.125 user 0.000 sys 0.205 real
fetch_ref: 2048 calls 0.025 user 0.009 sys 0.019 real
fetch_vcf: 2048 calls 1.143 user 0.041 sys 1.236 real
idle: 61 calls 0.001 user 0.000 sys 31.009 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2195 calls 7.258 user 1.482 sys 9.287 real
overall: 2674978816 mem 13.844 user 10.517 sys 62.432 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