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/7f/e78904d2fdc1b0bef3e12f8cce9b7c/.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-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/e78904d2fdc1b0bef3e12f8cce9b7c/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr19_47340800-47341813.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr19_47340800-47341813.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr19_47340800-47341813.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr19:49136724, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 168
progress 10% @chr19:50625897, elapsed 0.0s, est remaining 0.2s, peak mem 70MB, user 0.0s, sys 0.0s, output queue size 764
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.1s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1130
progress 20% @chr19:54805951, elapsed 0.0s, est remaining 0.1s, peak mem 73MB, user 0.0s, sys 0.0s, output queue size 1514
progress 25% @chr19:56208449, elapsed 0.0s, est remaining 0.1s, peak mem 75MB, user 0.0s, sys 0.1s, output queue size 1959
progress 30% @chr19:58260851, elapsed 0.0s, est remaining 0.1s, peak mem 78MB, user 0.0s, sys 0.1s, output queue size 2198
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 103MB, user 0.5s, sys 0.2s, output queue size 84
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 159MB, user 1.4s, sys 0.2s, output queue size 106
progress 45% @chr21:42426697, elapsed 0.8s, est remaining 1.0s, peak mem 270MB, user 6.5s, sys 0.3s, output queue size 121
progress 50% @chr21:45515658, elapsed 1.0s, est remaining 1.0s, peak mem 270MB, user 8.4s, sys 0.3s, output queue size 115
progress 55% @chr22:19405786, elapsed 1.1s, est remaining 0.9s, peak mem 270MB, user 9.1s, sys 0.3s, output queue size 299
progress 60% @chr22:22201834, elapsed 1.1s, est remaining 0.7s, peak mem 270MB, user 9.2s, sys 0.3s, output queue size 781
progress 65% @chr22:23883772, elapsed 1.1s, est remaining 0.6s, peak mem 270MB, user 9.2s, sys 0.3s, output queue size 999
progress 70% @chr22:29288004, elapsed 1.1s, est remaining 0.5s, peak mem 270MB, user 9.2s, sys 0.4s, output queue size 1507
progress 75% @chr22:31836972, elapsed 1.1s, est remaining 0.4s, peak mem 270MB, user 9.2s, sys 0.4s, output queue size 2046
progress 80% @chr22:37970687, elapsed 1.1s, est remaining 0.3s, peak mem 270MB, user 9.2s, sys 0.4s, output queue size 2614
progress 85% @chr22:41252872, elapsed 1.2s, est remaining 0.2s, peak mem 270MB, user 9.2s, sys 0.4s, output queue size 3129
progress 90% @chr22:46256561, elapsed 1.2s, est remaining 0.1s, peak mem 270MB, user 9.2s, sys 0.5s, output queue size 3749
progress 95% @chr22:50730721, elapsed 1.2s, est remaining 0.1s, peak mem 270MB, user 9.2s, sys 0.5s, output queue size 388
progress 100% @chrY:57106333, elapsed 1.2s, est remaining 0.0s, peak mem 270MB, user 9.3s, sys 0.5s, output queue size 966
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: 12 max 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692772
output file size: 77725
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.534 user 0.012 sys 0.679 real
"assemble_addRead": 315 calls 0.010 user 0.000 sys 0.032 real
"assemble_buildGraph": 650 calls 0.198 user 0.003 sys 0.334 real
"assemble_computecigar": 513 calls 0.244 user 0.010 sys 0.367 real
"assemble_kg_build_calcsize": 650 calls 0.150 user 0.000 sys 0.183 real
"assemble_kg_build_clear": 775 calls 0.026 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.172 user 0.004 sys 0.148 real
"assemble_kg_build_threading": 525 calls 0.047 user 0.003 sys 0.147 real
"assemble_kg_op1": 525 calls 0.012 user 0.001 sys 0.032 real
"assemble_kg_op2": 525 calls 0.010 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.000 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.034 user 0.000 sys 0.041 real
"assemble_sg_create": 513 calls 0.048 user 0.003 sys 0.052 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.276 user 0.010 sys 0.386 real
active: 19646 calls 0.000 user 0.000 sys 0.014 real
advance: 10022 calls 2.306 user 0.132 sys 3.024 real
annotate: 358 calls 0.005 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.820 user 0.022 sys 1.099 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.233 user 0.001 sys 0.295 real
calc_region: 312 calls 3.580 user 0.012 sys 3.899 real
call_region: 312 calls 0.025 user 0.000 sys 0.050 real
clip_region: 627 calls 0.017 user 0.000 sys 0.061 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.010 user 0.000 sys 1.237 real
fetch: 19646 calls 0.175 user 0.015 sys 0.128 real
fetch_db: 312 calls 0.018 user 0.000 sys 0.081 real
fetch_ref: 19961 calls 0.033 user 0.006 sys 0.077 real
fetch_region: 315 calls 0.005 user 0.000 sys 0.013 real
idle: 39 calls 0.003 user 0.001 sys 13.133 real
init: 1 calls 0.020 user 0.020 sys 0.045 real
pairhmm: 1803 calls 6.457 user 0.005 sys 6.953 real
realign: 598 calls 0.432 user 0.003 sys 0.516 real
region: 19646 calls 6.210 user 0.053 sys 6.128 real
tracker: 19646 calls 0.008 user 0.002 sys 0.024 real
trim_region: 315 calls 0.017 user 0.000 sys 0.004 real
overall: 283369472 mem 12.619 user 0.931 sys 2.353 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory