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/6d/e635a85e528d7611d80f1cdf043484/.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/0e/1efc95d887ebdaf1c9892b5421119a/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/1efc95d887ebdaf1c9892b5421119a/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr4_30730753-30730788.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6d/e635a85e528d7611d80f1cdf043484/.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 (9 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr4_30730753-30730788.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86774373, elapsed 0.1s, est remaining 1.0s, peak mem 75MB, user 0.0s, sys 0.2s, output queue size 1263
progress 10% @chr4:152346894, elapsed 0.1s, est remaining 0.9s, peak mem 78MB, user 0.0s, sys 0.4s, output queue size 3659
progress 15% @chr5:36177185, elapsed 0.2s, est remaining 0.9s, peak mem 93MB, user 0.0s, sys 0.7s, output queue size 6131
progress 20% @chr5:91153221, elapsed 0.2s, est remaining 0.8s, peak mem 96MB, user 0.1s, sys 1.0s, output queue size 8707
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 0.8s, peak mem 114MB, user 0.1s, sys 1.2s, output queue size 11117
progress 30% @chr5:177302397, elapsed 0.3s, est remaining 0.7s, peak mem 117MB, user 0.1s, sys 1.4s, output queue size 13228
progress 35% @chr6:30948547, elapsed 0.4s, est remaining 0.7s, peak mem 129MB, user 0.1s, sys 1.7s, output queue size 15421
progress 40% @chr6:43645099, elapsed 0.4s, est remaining 0.6s, peak mem 135MB, user 0.2s, sys 1.9s, output queue size 17967
progress 45% @chr6:106530176, elapsed 0.5s, est remaining 0.6s, peak mem 156MB, user 0.2s, sys 2.2s, output queue size 20431
progress 50% @chr6:149450683, elapsed 0.5s, est remaining 0.5s, peak mem 159MB, user 0.2s, sys 2.4s, output queue size 22530
progress 55% @chr7:13911239, elapsed 0.6s, est remaining 0.5s, peak mem 165MB, user 0.3s, sys 2.5s, output queue size 24791
progress 60% @chr7:64077276, elapsed 0.6s, est remaining 0.4s, peak mem 174MB, user 0.3s, sys 2.7s, output queue size 26860
progress 65% @chr7:100951841, elapsed 0.7s, est remaining 0.4s, peak mem 183MB, user 0.3s, sys 3.0s, output queue size 1441
progress 70% @chr7:139283024, elapsed 0.7s, est remaining 0.3s, peak mem 198MB, user 0.3s, sys 3.1s, output queue size 3803
progress 75% @chr8:13102790, elapsed 0.8s, est remaining 0.3s, peak mem 207MB, user 0.4s, sys 3.3s, output queue size 5860
progress 80% @chr8:38819522, elapsed 0.8s, est remaining 0.2s, peak mem 216MB, user 0.4s, sys 3.4s, output queue size 7484
progress 85% @chrX:15543071, elapsed 0.9s, est remaining 0.2s, peak mem 225MB, user 0.4s, sys 3.7s, output queue size 9996
progress 90% @chrX:50813902, elapsed 0.9s, est remaining 0.1s, peak mem 234MB, user 0.4s, sys 4.0s, output queue size 12364
progress 95% @chrX:111718112, elapsed 1.0s, est remaining 0.1s, peak mem 237MB, user 0.5s, sys 4.2s, output queue size 14290
progress 100% @chrX:156009816, elapsed 1.0s, est remaining 0.0s, peak mem 243MB, user 0.5s, sys 4.4s, output queue size 16510
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
cpu vendor: GenuineIntel
 signature: 000a06d1
  features: bfebfbff 7ffefbff
  extended: f3bfb7ef fb417ffe
  amd bits: 2c100800 00000121
     brand: Intel(R) Xeon(R) 6975P-C
threads: 12 max 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 71692776
output file size: 22309
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.000 user 0.000 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.007 user 0.000 sys 0.014 real
advance: 47638 calls 0.011 user 0.007 sys 0.023 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.000 real
calc: 93348 calls 0.009 user 0.012 sys 0.014 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.002 sys 1.939 real
fetch: 93348 calls 0.000 user 0.009 sys 0.015 real
fetch_ref: 93349 calls 0.108 user 0.105 sys 0.355 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.004 user 0.059 sys 23.349 real
init: 1 calls 0.039 user 0.001 sys 0.041 real
region: 93348 calls 0.009 user 0.017 sys 0.017 real
tracker: 93348 calls 0.027 user 0.008 sys 0.080 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 254976000 mem 1.011 user 6.389 sys 3.055 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory