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/19/0a75e332a027037fb2ea9aacaa5f43/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/regression_intervals/scatter/chr21_44120631-44120778.bed.gz
  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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/0a75e332a027037fb2ea9aacaa5f43/.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 chr21_44120631-44120778.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant HCC1395_BL.haplotyper.chr21_44120631-44120778.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr21:44222913, elapsed 0.0s, est remaining 0.2s, peak mem 82MB, user 0.0s, sys 0.0s, output queue size 2
progress 10% @chr21:44322133, elapsed 0.0s, est remaining 0.3s, peak mem 99MB, user 0.1s, sys 0.0s, output queue size 40
progress 15% @chr21:44236867, elapsed 0.1s, est remaining 0.3s, peak mem 117MB, user 0.3s, sys 0.0s, output queue size 70
progress 20% @chr21:44456645, elapsed 0.1s, est remaining 0.2s, peak mem 123MB, user 0.4s, sys 0.0s, output queue size 97
progress 25% @chr21:44550691, elapsed 0.1s, est remaining 0.2s, peak mem 150MB, user 0.5s, sys 0.0s, output queue size 108
progress 33% @chr21:44224713, elapsed 0.1s, est remaining 0.3s, peak mem 166MB, user 0.7s, sys 0.1s, output queue size 111
progress 35% @chr21:44579763, elapsed 0.2s, est remaining 0.4s, peak mem 214MB, user 1.0s, sys 0.1s, output queue size 6
progress 41% @chr21:44573759, elapsed 0.2s, est remaining 0.3s, peak mem 216MB, user 1.7s, sys 0.1s, output queue size 21
progress 45% @chr21:44900320, elapsed 0.2s, est remaining 0.3s, peak mem 216MB, user 2.0s, sys 0.1s, output queue size 42
progress 50% @chr21:45287741, elapsed 0.2s, est remaining 0.2s, peak mem 216MB, user 2.1s, sys 0.1s, output queue size 70
progress 55% @chr21:45492535, elapsed 0.3s, est remaining 0.2s, peak mem 216MB, user 2.3s, sys 0.1s, output queue size 39
progress 60% @chr21:45909355, elapsed 0.3s, est remaining 0.2s, peak mem 219MB, user 2.5s, sys 0.1s, output queue size 29
progress 65% @chr21:46122108, elapsed 0.3s, est remaining 0.2s, peak mem 220MB, user 2.7s, sys 0.1s, output queue size 11
progress 70% @chr21:46131954, elapsed 0.3s, est remaining 0.1s, peak mem 223MB, user 2.8s, sys 0.1s, output queue size 32
progress 75% @chr21:46258939, elapsed 0.3s, est remaining 0.1s, peak mem 223MB, user 3.0s, sys 0.1s, output queue size 53
progress 80% @chr21:46125785, elapsed 0.4s, est remaining 0.1s, peak mem 225MB, user 3.2s, sys 0.1s, output queue size 84
progress 85% @chr21:46399590, elapsed 0.4s, est remaining 0.1s, peak mem 225MB, user 3.3s, sys 0.1s, output queue size 30
progress 90% @chr21:46430010, elapsed 0.4s, est remaining 0.0s, peak mem 225MB, user 3.5s, sys 0.1s, output queue size 25
progress 95% @chr21:46545881, elapsed 0.4s, est remaining 0.0s, peak mem 225MB, user 3.5s, sys 0.1s, output queue size 53
progress 100% @chr21:46602278, elapsed 0.4s, est remaining 0.0s, peak mem 225MB, user 3.7s, sys 0.2s, output queue size 11
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 163002590
output file size: 38711
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.135 user 0.004 sys 0.219 real
"assemble_addRead": 96 calls 0.000 user 0.000 sys 0.010 real
"assemble_buildGraph": 205 calls 0.064 user 0.000 sys 0.110 real
"assemble_computecigar": 140 calls 0.077 user 0.017 sys 0.137 real
"assemble_kg_build_calcsize": 205 calls 0.014 user 0.000 sys 0.065 real
"assemble_kg_build_clear": 265 calls 0.002 user 0.000 sys 0.004 real
"assemble_kg_build_prepare": 410 calls 0.051 user 0.003 sys 0.050 real
"assemble_kg_build_threading": 145 calls 0.041 user 0.000 sys 0.043 real
"assemble_kg_op1": 145 calls 0.014 user 0.000 sys 0.010 real
"assemble_kg_op2": 145 calls 0.000 user 0.000 sys 0.003 real
"assemble_kg_op3": 145 calls 0.000 user 0.000 sys 0.003 real
"assemble_sg_clean": 140 calls 0.000 user 0.000 sys 0.012 real
"assemble_sg_create": 140 calls 0.004 user 0.001 sys 0.015 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.077 user 0.017 sys 0.142 real
active: 1044 calls 0.000 user 0.000 sys 0.003 real
advance: 528 calls 1.083 user 0.042 sys 1.403 real
annotate: 105 calls 0.000 user 0.000 sys 0.009 real
assemble_region: 96 calls 0.212 user 0.021 sys 0.372 real
build_variants: 95 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.128 user 0.000 sys 0.120 real
calc_region: 95 calls 1.414 user 0.049 sys 1.563 real
call_region: 95 calls 0.000 user 0.000 sys 0.015 real
clip_region: 191 calls 0.018 user 0.000 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.001 real
execute: 1 calls 0.006 user 0.002 sys 0.437 real
fetch: 1044 calls 0.065 user 0.000 sys 0.054 real
fetch_db: 95 calls 0.020 user 0.000 sys 0.029 real
fetch_ref: 1140 calls 0.001 user 0.000 sys 0.005 real
fetch_region: 96 calls 0.000 user 0.000 sys 0.005 real
idle: 48 calls 0.048 user 0.000 sys 12.512 real
init: 1 calls 0.030 user 0.010 sys 0.041 real
pairhmm: 430 calls 2.394 user 0.044 sys 2.708 real
realign: 197 calls 0.155 user 0.003 sys 0.168 real
region: 1044 calls 2.360 user 0.075 sys 2.416 real
tracker: 1044 calls 0.000 user 0.000 sys 0.003 real
trim_region: 96 calls 0.000 user 0.000 sys 0.002 real
overall: 236068864 mem 4.877 user 0.207 sys 1.543 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory