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/84/c5cda5b18933d1f4ee3d52c6c5a477/Sig_18_tissue.md.bam.bai
  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/84/c5cda5b18933d1f4ee3d52c6c5a477/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b4/41308b789387c5f697041128a8daf6/.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/b4/41308b789387c5f697041128a8daf6/.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 Sig_18_tissue.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 Sig_18_tissue.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119421809, elapsed 0.1s, est remaining 1.3s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 103
progress 10% @chr2:20260337, elapsed 0.1s, est remaining 1.2s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 117
progress 15% @chr2:189034916, elapsed 0.2s, est remaining 1.2s, peak mem 182MB, user 0.0s, sys 0.0s, output queue size 1072
progress 20% @chr3:97871842, elapsed 0.3s, est remaining 1.1s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 11542
progress 25% @chr4:88457270, elapsed 0.3s, est remaining 1.0s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 8733
progress 30% @chr5:147399082, elapsed 0.4s, est remaining 1.0s, peak mem 209MB, user 0.0s, sys 0.0s, output queue size 18775
progress 35% @chr6:127135950, elapsed 0.5s, est remaining 0.9s, peak mem 209MB, user 0.0s, sys 0.0s, output queue size 856
progress 40% @chr7:128775439, elapsed 0.5s, est remaining 0.8s, peak mem 218MB, user 0.0s, sys 0.0s, output queue size 10302
progress 45% @chr9:2028988, elapsed 0.6s, est remaining 0.7s, peak mem 371MB, user 0.0s, sys 0.1s, output queue size 19668
progress 50% @chr10:32346763, elapsed 0.7s, est remaining 0.7s, peak mem 407MB, user 0.0s, sys 0.1s, output queue size 29606
progress 55% @chr11:48121003, elapsed 0.7s, est remaining 0.6s, peak mem 443MB, user 0.0s, sys 0.1s, output queue size 40072
progress 60% @chr12:22471399, elapsed 0.7s, est remaining 0.5s, peak mem 446MB, user 0.0s, sys 0.1s, output queue size 49656
progress 65% @chr13:48706818, elapsed 0.8s, est remaining 0.4s, peak mem 452MB, user 0.0s, sys 0.1s, output queue size 60676
progress 70% @chr15:42717977, elapsed 0.8s, est remaining 0.4s, peak mem 452MB, user 0.0s, sys 0.1s, output queue size 70711
progress 75% @chr16:30946730, elapsed 0.9s, est remaining 0.3s, peak mem 452MB, user 0.0s, sys 0.1s, output queue size 80277
progress 80% @chr17:42507520, elapsed 0.9s, est remaining 0.2s, peak mem 461MB, user 0.0s, sys 0.1s, output queue size 90961
progress 85% @chr19:5641740, elapsed 1.0s, est remaining 0.2s, peak mem 461MB, user 0.0s, sys 0.1s, output queue size 101370
progress 90% @chr19:55678527, elapsed 1.0s, est remaining 0.1s, peak mem 461MB, user 0.0s, sys 0.1s, output queue size 110872
progress 95% @chr22:36937342, elapsed 1.4s, est remaining 0.1s, peak mem 2492MB, user 7.3s, sys 1.7s, output queue size 3225
progress 100% @chr6_GL000254v2_alt:3877871, elapsed 1.5s, est remaining 0.0s, peak mem 2492MB, user 7.4s, sys 1.7s, output queue size 8498
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 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 50047052
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.759 user 0.105 sys 2.178 real
done: 1 calls 0.469 user 0.159 sys 0.634 real
execute: 1 calls 0.005 user 0.001 sys 1.472 real
fetch_reads: 208647 calls 0.082 user 0.000 sys 0.169 real
fetch_ref: 2079 calls 0.002 user 0.006 sys 0.027 real
fetch_vcf: 2079 calls 0.708 user 0.043 sys 0.974 real
idle: 92 calls 0.003 user 0.001 sys 31.787 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 5.933 user 1.523 sys 8.067 real
overall: 2613551104 mem 12.399 user 12.733 sys 2.871 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