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/cc/de32157441b4354414137b7b901290/.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/cc/de32157441b4354414137b7b901290/.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% @chr21:44256067, elapsed 0.0s, est remaining 0.4s, peak mem 66MB, user 0.1s, sys 0.0s, output queue size 4
progress 10% @chr21:44231276, elapsed 0.1s, est remaining 0.5s, peak mem 84MB, user 0.3s, sys 0.0s, output queue size 39
progress 15% @chr21:44390904, elapsed 0.1s, est remaining 0.4s, peak mem 96MB, user 0.4s, sys 0.1s, output queue size 69
progress 20% @chr21:44509199, elapsed 0.1s, est remaining 0.4s, peak mem 102MB, user 0.5s, sys 0.1s, output queue size 101
progress 25% @chr21:44550691, elapsed 0.1s, est remaining 0.3s, peak mem 111MB, user 0.6s, sys 0.1s, output queue size 108
progress 34% @chr21:44224713, elapsed 0.3s, est remaining 0.5s, peak mem 177MB, user 1.2s, sys 0.2s, output queue size 112
progress 35% @chr21:44681833, elapsed 0.3s, est remaining 0.5s, peak mem 177MB, user 1.3s, sys 0.2s, output queue size 7
progress 40% @chr21:44889276, elapsed 0.3s, est remaining 0.4s, peak mem 177MB, user 1.8s, sys 0.2s, output queue size 30
progress 45% @chr21:44910725, elapsed 0.3s, est remaining 0.4s, peak mem 177MB, user 2.2s, sys 0.2s, output queue size 54
progress 50% @chr21:44637418, elapsed 0.3s, est remaining 0.3s, peak mem 177MB, user 2.7s, sys 0.2s, output queue size 71
progress 55% @chr21:44539302, elapsed 0.3s, est remaining 0.3s, peak mem 177MB, user 3.0s, sys 0.2s, output queue size 105
progress 60% @chr21:45986526, elapsed 0.4s, est remaining 0.2s, peak mem 177MB, user 3.2s, sys 0.2s, output queue size 31
progress 65% @chr21:46118614, elapsed 0.4s, est remaining 0.2s, peak mem 177MB, user 3.5s, sys 0.3s, output queue size 16
progress 70% @chr21:46191881, elapsed 0.4s, est remaining 0.2s, peak mem 180MB, user 3.6s, sys 0.3s, output queue size 32
progress 75% @chr21:46260793, elapsed 0.4s, est remaining 0.1s, peak mem 180MB, user 3.7s, sys 0.3s, output queue size 54
progress 80% @chr21:46125785, elapsed 0.5s, est remaining 0.1s, peak mem 180MB, user 4.1s, sys 0.3s, output queue size 85
progress 85% @chr21:46389199, elapsed 0.5s, est remaining 0.1s, peak mem 180MB, user 4.2s, sys 0.3s, output queue size 25
progress 90% @chr21:46444694, elapsed 0.5s, est remaining 0.1s, peak mem 180MB, user 4.4s, sys 0.3s, output queue size 25
progress 95% @chr21:46551824, elapsed 0.5s, est remaining 0.0s, peak mem 180MB, user 4.5s, sys 0.3s, output queue size 52
progress 100% @chr21:46602278, elapsed 0.6s, est remaining 0.0s, peak mem 180MB, user 4.6s, sys 0.3s, output queue size 11
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
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: 163002590
output file size: 38710
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.182 user 0.018 sys 0.291 real
"assemble_addRead": 96 calls 0.004 user 0.000 sys 0.017 real
"assemble_buildGraph": 205 calls 0.070 user 0.010 sys 0.142 real
"assemble_computecigar": 140 calls 0.125 user 0.025 sys 0.191 real
"assemble_kg_build_calcsize": 205 calls 0.048 user 0.007 sys 0.081 real
"assemble_kg_build_clear": 265 calls 0.002 user 0.001 sys 0.007 real
"assemble_kg_build_prepare": 410 calls 0.054 user 0.006 sys 0.070 real
"assemble_kg_build_threading": 145 calls 0.022 user 0.003 sys 0.058 real
"assemble_kg_op1": 145 calls 0.011 user 0.000 sys 0.014 real
"assemble_kg_op2": 145 calls 0.001 user 0.000 sys 0.004 real
"assemble_kg_op3": 145 calls 0.000 user 0.000 sys 0.004 real
"assemble_sg_clean": 140 calls 0.012 user 0.000 sys 0.014 real
"assemble_sg_create": 140 calls 0.019 user 0.001 sys 0.019 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.136 user 0.025 sys 0.197 real
active: 1044 calls 0.000 user 0.000 sys 0.006 real
advance: 528 calls 1.388 user 0.111 sys 1.780 real
annotate: 105 calls 0.001 user 0.000 sys 0.014 real
assemble_region: 96 calls 0.322 user 0.043 sys 0.506 real
build_variants: 95 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.132 user 0.012 sys 0.180 real
calc_region: 95 calls 1.793 user 0.057 sys 1.994 real
call_region: 95 calls 0.006 user 0.000 sys 0.023 real
clip_region: 191 calls 0.021 user 0.001 sys 0.026 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.002 user 0.001 sys 0.568 real
fetch: 1044 calls 0.075 user 0.005 sys 0.115 real
fetch_db: 95 calls 0.020 user 0.001 sys 0.038 real
fetch_ref: 1140 calls 0.033 user 0.000 sys 0.007 real
fetch_region: 96 calls 0.010 user 0.000 sys 0.005 real
idle: 49 calls 0.043 user 0.003 sys 12.727 real
init: 1 calls 0.033 user 0.022 sys 0.053 real
pairhmm: 430 calls 3.115 user 0.108 sys 3.406 real
realign: 197 calls 0.144 user 0.005 sys 0.212 real
region: 1044 calls 2.911 user 0.120 sys 3.132 real
tracker: 1044 calls 0.003 user 0.000 sys 0.005 real
trim_region: 96 calls 0.002 user 0.000 sys 0.002 real
overall: 188882944 mem 6.098 user 0.411 sys 1.691 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory