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/98/e1c2a3972c64d0745e49884e28896c/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/98/e1c2a3972c64d0745e49884e28896c/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/c734bcdc9fc0aa72bf133c8da3c35a/.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/65/c734bcdc9fc0aa72bf133c8da3c35a/.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% @chr1:119768741, elapsed 0.0s, est remaining 0.7s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 7963
progress 10% @chr2:19994299, elapsed 0.1s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 6521
progress 15% @chr2:189042720, elapsed 0.1s, est remaining 0.6s, peak mem 181MB, user 0.0s, sys 0.0s, output queue size 16917
progress 20% @chr3:97871842, elapsed 0.1s, est remaining 0.5s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 27387
progress 25% @chr4:88440148, elapsed 0.2s, est remaining 0.5s, peak mem 190MB, user 0.0s, sys 0.0s, output queue size 37650
progress 30% @chr5:147375090, elapsed 0.2s, est remaining 0.5s, peak mem 208MB, user 0.0s, sys 0.0s, output queue size 47691
progress 35% @chr6:127137390, elapsed 0.2s, est remaining 0.4s, peak mem 213MB, user 0.0s, sys 0.0s, output queue size 2873
progress 40% @chr7:128792320, elapsed 0.3s, est remaining 0.4s, peak mem 222MB, user 0.0s, sys 0.0s, output queue size 12360
progress 45% @chr9:2028988, elapsed 0.3s, est remaining 0.3s, peak mem 339MB, user 0.0s, sys 0.0s, output queue size 21733
progress 50% @chr10:32284698, elapsed 0.3s, est remaining 0.3s, peak mem 411MB, user 0.0s, sys 0.1s, output queue size 31670
progress 55% @chr11:48324941, elapsed 0.3s, est remaining 0.3s, peak mem 447MB, user 0.0s, sys 0.1s, output queue size 42132
progress 60% @chr12:22058567, elapsed 0.4s, est remaining 0.2s, peak mem 450MB, user 0.0s, sys 0.1s, output queue size 51716
progress 65% @chr13:49267490, elapsed 0.4s, est remaining 0.2s, peak mem 478MB, user 0.0s, sys 0.1s, output queue size 62733
progress 70% @chr15:42684116, elapsed 0.4s, est remaining 0.2s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 72792
progress 75% @chr16:30902078, elapsed 0.5s, est remaining 0.2s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 82333
progress 80% @chr17:42337727, elapsed 0.5s, est remaining 0.1s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 93027
progress 85% @chr19:5657241, elapsed 0.5s, est remaining 0.1s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 103431
progress 90% @chr19:55642509, elapsed 0.6s, est remaining 0.1s, peak mem 522MB, user 0.0s, sys 0.1s, output queue size 112932
progress 95% @chr22:37066826, elapsed 1.0s, est remaining 0.1s, peak mem 2533MB, user 7.9s, sys 1.5s, output queue size 3245
progress 100% @chr21:41501693, elapsed 1.0s, est remaining 0.0s, peak mem 2533MB, user 8.2s, sys 1.5s, output queue size 12805
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 50047074
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.489 user 0.099 sys 2.242 real
done: 1 calls 0.233 user 0.119 sys 0.352 real
execute: 1 calls 0.005 user 0.001 sys 1.007 real
fetch_reads: 208647 calls 0.102 user 0.001 sys 0.205 real
fetch_ref: 2079 calls 0.006 user 0.018 sys 0.018 real
fetch_vcf: 2079 calls 0.880 user 0.030 sys 0.996 real
idle: 92 calls 0.003 user 0.002 sys 31.623 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 6.791 user 1.392 sys 8.397 real
overall: 2656706560 mem 11.793 user 14.506 sys 2.378 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