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/26/bdb804792874396554f8c9a3111296/HCC1395_tumor.md.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/70/abbc3e865441056b5cbdbb57e966eb/.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/70/abbc3e865441056b5cbdbb57e966eb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/bdb804792874396554f8c9a3111296/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.
progress 5% @chr1:119911554, elapsed 0.0s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2711
progress 10% @chr2:17780621, elapsed 0.1s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 6825
progress 15% @chr2:189039272, elapsed 0.1s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 17215
progress 20% @chr3:97871842, elapsed 0.1s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 5961
progress 25% @chr4:88268741, elapsed 0.2s, est remaining 0.5s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 16229
progress 30% @chr5:147418447, elapsed 0.2s, est remaining 0.5s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 26277
progress 35% @chr6:127137390, elapsed 0.2s, est remaining 0.4s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 36213
progress 40% @chr7:128809450, elapsed 0.3s, est remaining 0.4s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 45700
progress 45% @chr9:1056216, elapsed 0.3s, est remaining 0.4s, peak mem 333MB, user 0.0s, sys 0.0s, output queue size 55075
progress 50% @chr10:32451643, elapsed 0.3s, est remaining 0.3s, peak mem 349MB, user 0.0s, sys 0.0s, output queue size 2033
progress 55% @chr11:48167204, elapsed 0.4s, est remaining 0.3s, peak mem 349MB, user 0.0s, sys 0.0s, output queue size 12488
progress 60% @chr12:21925942, elapsed 0.4s, est remaining 0.3s, peak mem 355MB, user 0.0s, sys 0.0s, output queue size 22034
progress 65% @chr13:49220338, elapsed 0.4s, est remaining 0.2s, peak mem 358MB, user 0.0s, sys 0.0s, output queue size 33080
progress 70% @chr15:42684116, elapsed 0.5s, est remaining 0.2s, peak mem 367MB, user 0.0s, sys 0.0s, output queue size 43129
progress 75% @chr16:30964094, elapsed 0.5s, est remaining 0.2s, peak mem 367MB, user 0.0s, sys 0.0s, output queue size 52693
progress 80% @chr17:42554402, elapsed 0.5s, est remaining 0.1s, peak mem 367MB, user 0.0s, sys 0.0s, output queue size 63370
progress 85% @chr19:5650978, elapsed 0.6s, est remaining 0.1s, peak mem 378MB, user 0.0s, sys 0.0s, output queue size 73785
progress 90% @chr19:55602113, elapsed 0.6s, est remaining 0.1s, peak mem 378MB, user 0.0s, sys 0.0s, output queue size 83283
progress 95% @chr22:36875653, elapsed 0.9s, est remaining 0.0s, peak mem 2521MB, user 6.5s, sys 1.9s, output queue size 3221
progress 100% @chr6_GL000251v2_alt:3946951, elapsed 1.0s, est remaining 0.0s, peak mem 2521MB, user 6.6s, sys 1.9s, output queue size 6866
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 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 50813912
reads: 1001320
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.900 user 0.100 sys 2.169 real
done: 1 calls 0.226 user 0.128 sys 0.354 real
execute: 1 calls 0.012 user 0.001 sys 0.990 real
fetch_reads: 208647 calls 0.067 user 0.000 sys 0.144 real
fetch_ref: 2048 calls 0.004 user 0.008 sys 0.023 real
fetch_vcf: 2048 calls 0.872 user 0.031 sys 0.950 real
idle: 92 calls 0.003 user 0.001 sys 31.508 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2195 calls 4.256 user 1.720 sys 6.779 real
overall: 2644180992 mem 10.086 user 7.383 sys 2.354 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