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/ce/c0b237b5a2ed301484d67c0460c0fd/.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/ce/c0b237b5a2ed301484d67c0460c0fd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/0dba0120ac4c8b91bbd8e39d57d28c/Sig_18_Blood.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/0dba0120ac4c8b91bbd8e39d57d28c/Sig_18_Blood.md.bam.bai
  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_Blood.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_Blood.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 0.0s, est remaining 0.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 487
progress 10% @chr2:20033205, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 10528
progress 15% @chr2:189052911, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 8152
progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 18618
progress 25% @chr4:88442234, elapsed 0.2s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 28884
progress 30% @chr5:146514854, elapsed 0.3s, est remaining 0.6s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 5330
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 15284
progress 40% @chr7:128772540, elapsed 0.3s, est remaining 0.5s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 24766
progress 45% @chr9:730051, elapsed 0.4s, est remaining 0.5s, peak mem 283MB, user 0.0s, sys 0.1s, output queue size 34123
progress 50% @chr10:29550597, elapsed 0.4s, est remaining 0.4s, peak mem 292MB, user 0.0s, sys 0.1s, output queue size 44077
progress 55% @chr11:48245104, elapsed 0.5s, est remaining 0.4s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 54534
progress 60% @chr12:21475669, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 64086
progress 65% @chr13:49222040, elapsed 0.5s, est remaining 0.3s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 75136
progress 70% @chr15:42958013, elapsed 0.6s, est remaining 0.2s, peak mem 301MB, user 0.0s, sys 0.1s, output queue size 85234
progress 75% @chr16:30942116, elapsed 0.6s, est remaining 0.2s, peak mem 306MB, user 0.0s, sys 0.1s, output queue size 3350
progress 80% @chr17:42543028, elapsed 0.6s, est remaining 0.2s, peak mem 306MB, user 0.0s, sys 0.1s, output queue size 14044
progress 85% @chr19:5661518, elapsed 0.7s, est remaining 0.1s, peak mem 333MB, user 0.0s, sys 0.1s, output queue size 24450
progress 90% @chr19:55688870, elapsed 0.7s, est remaining 0.1s, peak mem 333MB, user 0.0s, sys 0.1s, output queue size 33948
progress 95% @chr22:36932722, elapsed 1.1s, est remaining 0.1s, peak mem 2515MB, user 6.7s, sys 2.5s, output queue size 3249
progress 100% @chr21:41501693, elapsed 1.1s, est remaining 0.0s, peak mem 2515MB, user 7.0s, sys 2.5s, 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: 52293961
reads: 1001133
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.853 user 0.107 sys 2.286 real
done: 1 calls 0.293 user 0.088 sys 0.386 real
execute: 1 calls 0.014 user 0.001 sys 1.150 real
fetch_reads: 208647 calls 0.075 user 0.000 sys 0.175 real
fetch_ref: 2072 calls 0.006 user 0.013 sys 0.026 real
fetch_vcf: 2072 calls 1.005 user 0.036 sys 1.006 real
idle: 95 calls 0.013 user 0.005 sys 32.092 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2257 calls 4.868 user 2.334 sys 7.941 real
overall: 2637991936 mem 10.955 user 10.807 sys 2.516 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