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/ab/115b64305d060833379ba5675af81f/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/ab/115b64305d060833379ba5675af81f/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/a49026cb49cc8dd6ad31be4a0e0bdf/.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/55/a49026cb49cc8dd6ad31be4a0e0bdf/.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% @chr1:119911554, elapsed 0.0s, est remaining 0.8s, peak mem 169MB, user 0.0s, sys 0.0s, output queue size 5956
progress 10% @chr2:17785862, elapsed 0.1s, est remaining 0.7s, peak mem 169MB, user 0.0s, sys 0.0s, output queue size 8753
progress 15% @chr2:189057320, elapsed 0.1s, est remaining 0.7s, peak mem 178MB, user 0.0s, sys 0.0s, output queue size 19140
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.6s, peak mem 187MB, user 0.0s, sys 0.0s, output queue size 4572
progress 25% @chr4:88437711, elapsed 0.2s, est remaining 0.6s, peak mem 187MB, user 0.0s, sys 0.0s, output queue size 14833
progress 30% @chr5:146458884, elapsed 0.2s, est remaining 0.5s, peak mem 205MB, user 0.0s, sys 0.0s, output queue size 24874
progress 35% @chr6:127985721, elapsed 0.3s, est remaining 0.5s, peak mem 205MB, user 0.0s, sys 0.0s, output queue size 34858
progress 40% @chr7:128811800, elapsed 0.3s, est remaining 0.4s, peak mem 214MB, user 0.0s, sys 0.0s, output queue size 44311
progress 45% @chr9:2028988, elapsed 0.3s, est remaining 0.4s, peak mem 361MB, user 0.0s, sys 0.0s, output queue size 53684
progress 50% @chr10:32037520, elapsed 0.4s, est remaining 0.4s, peak mem 403MB, user 0.0s, sys 0.1s, output queue size 63614
progress 55% @chr11:48245104, elapsed 0.4s, est remaining 0.3s, peak mem 439MB, user 0.0s, sys 0.1s, output queue size 74081
progress 60% @chr12:22453896, elapsed 0.4s, est remaining 0.3s, peak mem 448MB, user 0.0s, sys 0.1s, output queue size 7748
progress 65% @chr13:49220338, elapsed 0.5s, est remaining 0.3s, peak mem 478MB, user 0.0s, sys 0.1s, output queue size 18766
progress 70% @chr15:42684116, elapsed 0.5s, est remaining 0.2s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 28806
progress 75% @chr16:30930073, elapsed 0.5s, est remaining 0.2s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 38366
progress 80% @chr17:42543028, elapsed 0.6s, est remaining 0.1s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 49060
progress 85% @chr19:5667046, elapsed 0.6s, est remaining 0.1s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 59464
progress 90% @chr19:55695148, elapsed 0.6s, est remaining 0.1s, peak mem 520MB, user 0.0s, sys 0.1s, output queue size 68962
progress 95% @chr22:36762904, elapsed 1.0s, est remaining 0.1s, peak mem 2509MB, user 7.2s, sys 1.6s, output queue size 3225
progress 100% @chrY:57187928, elapsed 1.1s, est remaining 0.0s, peak mem 2509MB, user 7.3s, sys 1.6s, output queue size 7050
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 50047057
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.550 user 0.063 sys 2.049 real
done: 1 calls 0.276 user 0.079 sys 0.363 real
execute: 1 calls 0.004 user 0.001 sys 1.065 real
fetch_reads: 208647 calls 0.070 user 0.000 sys 0.143 real
fetch_ref: 2079 calls 0.027 user 0.010 sys 0.023 real
fetch_vcf: 2079 calls 0.757 user 0.030 sys 0.935 real
idle: 92 calls 0.002 user 0.002 sys 31.608 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 5.879 user 1.462 sys 7.896 real
overall: 2631118848 mem 10.944 user 13.458 sys 2.432 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