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/6f/b5caf8e1af69915d3b491b288a95f0/.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/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6f/b5caf8e1af69915d3b491b288a95f0/.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% @chr19:49118633, elapsed 0.0s, est remaining 0.4s, peak mem 69MB, user 0.0s, sys 0.0s, output queue size 382
progress 10% @chr19:50629784, elapsed 0.0s, est remaining 0.3s, peak mem 69MB, user 0.0s, sys 0.1s, output queue size 94
progress 15% @chr19:52553107, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 459
progress 20% @chr19:54813842, elapsed 0.0s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 846
progress 25% @chr19:56221575, elapsed 0.1s, est remaining 0.2s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 1283
progress 30% @chr19:58243965, elapsed 0.1s, est remaining 0.1s, peak mem 69MB, user 0.1s, sys 0.1s, output queue size 1526
progress 35% @chr21:29342399, elapsed 0.1s, est remaining 0.2s, peak mem 90MB, user 0.6s, sys 0.2s, output queue size 83
progress 40% @chr21:36460976, elapsed 0.3s, est remaining 0.4s, peak mem 138MB, user 1.5s, sys 0.2s, output queue size 107
progress 45% @chr21:41497133, elapsed 0.9s, est remaining 1.1s, peak mem 252MB, user 6.8s, sys 0.3s, output queue size 106
progress 50% @chr21:44539302, elapsed 1.1s, est remaining 1.1s, peak mem 254MB, user 8.6s, sys 0.4s, output queue size 117
progress 55% @chr22:18606515, elapsed 1.2s, est remaining 1.0s, peak mem 254MB, user 9.3s, sys 0.4s, output queue size 195
progress 60% @chr22:22380959, elapsed 1.2s, est remaining 0.8s, peak mem 254MB, user 9.3s, sys 0.4s, output queue size 695
progress 65% @chr22:23894772, elapsed 1.3s, est remaining 0.7s, peak mem 254MB, user 9.3s, sys 0.4s, output queue size 894
progress 70% @chr22:29288004, elapsed 1.3s, est remaining 0.5s, peak mem 254MB, user 9.3s, sys 0.4s, output queue size 1399
progress 75% @chr22:31845018, elapsed 1.3s, est remaining 0.4s, peak mem 254MB, user 9.4s, sys 0.5s, output queue size 1943
progress 80% @chr22:37956773, elapsed 1.3s, est remaining 0.3s, peak mem 254MB, user 9.4s, sys 0.5s, output queue size 2505
progress 85% @chr22:41261446, elapsed 1.3s, est remaining 0.2s, peak mem 254MB, user 9.4s, sys 0.5s, output queue size 264
progress 90% @chr22:46256561, elapsed 1.4s, est remaining 0.2s, peak mem 254MB, user 9.4s, sys 0.6s, output queue size 872
progress 95% @chr22:50730721, elapsed 1.4s, est remaining 0.1s, peak mem 254MB, user 9.4s, sys 0.6s, output queue size 1448
progress 100% @chr6_GL000251v2_alt:3935152, elapsed 1.4s, est remaining 0.0s, peak mem 254MB, user 9.5s, sys 0.7s, output queue size 2026
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: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692772
output file size: 77724
reads: 1001089
contig: 9624 intervals 1921786 bases
"assemble": 315 calls 0.455 user 0.035 sys 0.696 real
"assemble_addRead": 315 calls 0.010 user 0.000 sys 0.033 real
"assemble_buildGraph": 650 calls 0.142 user 0.007 sys 0.341 real
"assemble_computecigar": 513 calls 0.271 user 0.028 sys 0.376 real
"assemble_kg_build_calcsize": 650 calls 0.061 user 0.000 sys 0.185 real
"assemble_kg_build_clear": 775 calls 0.011 user 0.000 sys 0.015 real
"assemble_kg_build_prepare": 1300 calls 0.166 user 0.019 sys 0.156 real
"assemble_kg_build_threading": 525 calls 0.075 user 0.007 sys 0.151 real
"assemble_kg_op1": 525 calls 0.025 user 0.000 sys 0.033 real
"assemble_kg_op2": 525 calls 0.013 user 0.000 sys 0.009 real
"assemble_kg_op3": 525 calls 0.020 user 0.000 sys 0.011 real
"assemble_sg_clean": 513 calls 0.015 user 0.004 sys 0.041 real
"assemble_sg_create": 513 calls 0.057 user 0.005 sys 0.054 real
"checkGraph": 315 calls 0.000 user 0.000 sys 0.001 real
"findHaplotype": 315 calls 0.281 user 0.028 sys 0.395 real
active: 19646 calls 0.000 user 0.000 sys 0.014 real
advance: 10022 calls 1.967 user 0.094 sys 3.061 real
annotate: 358 calls 0.016 user 0.000 sys 0.026 real
assemble_region: 315 calls 0.746 user 0.063 sys 1.127 real
build_variants: 312 calls 0.000 user 0.000 sys 0.001 real
calc: 19646 calls 0.206 user 0.001 sys 0.303 real
calc_region: 312 calls 3.927 user 0.025 sys 4.344 real
call_region: 312 calls 0.016 user 0.000 sys 0.050 real
clip_region: 627 calls 0.043 user 0.000 sys 0.063 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.006 user 0.003 sys 1.835 real
fetch: 19646 calls 0.209 user 0.013 sys 0.137 real
fetch_db: 312 calls 0.036 user 0.000 sys 0.085 real
fetch_ref: 19961 calls 0.001 user 0.004 sys 0.082 real
fetch_region: 315 calls 0.032 user 0.000 sys 0.014 real
idle: 39 calls 0.004 user 0.002 sys 17.289 real
init: 1 calls 0.020 user 0.020 sys 0.043 real
pairhmm: 1803 calls 6.568 user 0.031 sys 7.033 real
realign: 598 calls 0.350 user 0.002 sys 0.521 real
region: 19646 calls 5.925 user 0.085 sys 6.171 real
tracker: 19646 calls 0.011 user 0.001 sys 0.025 real
trim_region: 315 calls 0.000 user 0.000 sys 0.004 real
overall: 266428416 mem 12.712 user 1.137 sys 2.952 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory