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/60/7470c79045f038a00190ba06d78351/.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/60/7470c79045f038a00190ba06d78351/.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% @chr21:44254617, elapsed 0.0s, est remaining 0.3s, peak mem 72MB, user 0.0s, sys 0.0s, output queue size 1
progress 10% @chr21:44321729, elapsed 0.0s, est remaining 0.4s, peak mem 102MB, user 0.2s, sys 0.0s, output queue size 39
progress 15% @chr21:44395414, elapsed 0.1s, est remaining 0.3s, peak mem 108MB, user 0.3s, sys 0.0s, output queue size 71
progress 20% @chr21:44456645, elapsed 0.1s, est remaining 0.2s, peak mem 114MB, user 0.4s, sys 0.0s, output queue size 98
progress 26% @chr21:44591387, elapsed 0.1s, est remaining 0.2s, peak mem 147MB, user 0.5s, sys 0.0s, output queue size 108
progress 33% @chr21:44224713, elapsed 0.1s, est remaining 0.3s, peak mem 159MB, user 0.6s, sys 0.0s, output queue size 112
progress 35% @chr21:44697202, elapsed 0.1s, est remaining 0.3s, peak mem 162MB, user 0.7s, sys 0.0s, output queue size 7
progress 40% @chr21:44579763, elapsed 0.2s, est remaining 0.2s, peak mem 162MB, user 1.1s, sys 0.1s, output queue size 25
progress 45% @chr21:44666446, elapsed 0.2s, est remaining 0.3s, peak mem 201MB, user 1.6s, sys 0.1s, output queue size 51
progress 50% @chr21:45283383, elapsed 0.2s, est remaining 0.2s, peak mem 201MB, user 1.8s, sys 0.1s, output queue size 70
progress 55% @chr21:45455531, elapsed 0.3s, est remaining 0.2s, peak mem 201MB, user 1.9s, sys 0.1s, output queue size 111
progress 60% @chr21:45986944, elapsed 0.3s, est remaining 0.2s, peak mem 201MB, user 2.2s, sys 0.1s, output queue size 29
progress 65% @chr21:46119788, elapsed 0.3s, est remaining 0.2s, peak mem 201MB, user 2.4s, sys 0.1s, output queue size 11
progress 70% @chr21:46161379, elapsed 0.3s, est remaining 0.1s, peak mem 204MB, user 2.5s, sys 0.1s, output queue size 22
progress 75% @chr21:46246628, elapsed 0.3s, est remaining 0.1s, peak mem 204MB, user 2.6s, sys 0.1s, output queue size 54
progress 80% @chr21:46265925, elapsed 0.4s, est remaining 0.1s, peak mem 204MB, user 2.8s, sys 0.1s, output queue size 84
progress 85% @chr21:46390670, elapsed 0.4s, est remaining 0.1s, peak mem 204MB, user 3.1s, sys 0.1s, output queue size 22
progress 90% @chr21:46430010, elapsed 0.4s, est remaining 0.0s, peak mem 204MB, user 3.2s, sys 0.1s, output queue size 26
progress 95% @chr21:46551824, elapsed 0.4s, est remaining 0.0s, peak mem 204MB, user 3.4s, sys 0.1s, output queue size 30
progress 100% @chr21:46602278, elapsed 0.4s, est remaining 0.0s, peak mem 204MB, user 3.4s, sys 0.1s, output queue size 11
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: 163002590
output file size: 38710
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.153 user 0.004 sys 0.219 real
"assemble_addRead": 96 calls 0.020 user 0.000 sys 0.010 real
"assemble_buildGraph": 205 calls 0.103 user 0.004 sys 0.110 real
"assemble_computecigar": 140 calls 0.063 user 0.000 sys 0.139 real
"assemble_kg_build_calcsize": 205 calls 0.056 user 0.000 sys 0.065 real
"assemble_kg_build_clear": 265 calls 0.010 user 0.000 sys 0.004 real
"assemble_kg_build_prepare": 410 calls 0.009 user 0.000 sys 0.051 real
"assemble_kg_build_threading": 145 calls 0.047 user 0.004 sys 0.043 real
"assemble_kg_op1": 145 calls 0.003 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 0.010 user 0.000 sys 0.012 real
"assemble_sg_create": 140 calls 0.017 user 0.000 sys 0.015 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.074 user 0.000 sys 0.143 real
active: 1044 calls 0.020 user 0.000 sys 0.003 real
advance: 528 calls 1.223 user 0.074 sys 1.398 real
annotate: 105 calls 0.000 user 0.000 sys 0.009 real
assemble_region: 96 calls 0.247 user 0.004 sys 0.374 real
build_variants: 95 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.035 user 0.001 sys 0.118 real
calc_region: 95 calls 1.159 user 0.040 sys 1.320 real
call_region: 95 calls 0.000 user 0.000 sys 0.015 real
clip_region: 191 calls 0.001 user 0.000 sys 0.017 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.003 user 0.001 sys 0.435 real
fetch: 1044 calls 0.033 user 0.000 sys 0.052 real
fetch_db: 95 calls 0.012 user 0.001 sys 0.029 real
fetch_ref: 1140 calls 0.003 user 0.000 sys 0.005 real
fetch_region: 96 calls 0.000 user 0.000 sys 0.004 real
idle: 48 calls 0.050 user 0.000 sys 12.583 real
init: 1 calls 0.042 user 0.008 sys 0.044 real
pairhmm: 430 calls 2.342 user 0.063 sys 2.692 real
realign: 197 calls 0.079 user 0.001 sys 0.166 real
region: 1044 calls 2.100 user 0.069 sys 2.190 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: 214044672 mem 4.854 user 0.220 sys 1.541 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory