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/ce/08d84e56c283d8c0e58f0ca86ae1a5/.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-rnd-pltf-dev-nextflow-scratch-01/work/ce/08d84e56c283d8c0e58f0ca86ae1a5/.command.run
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam
  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 Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant Sig_18_Blood.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 85MB, user 0.1s, sys 0.0s, output queue size 1
progress 10% @chr21:44316244, elapsed 0.0s, est remaining 0.3s, peak mem 99MB, user 0.2s, sys 0.0s, output queue size 39
progress 15% @chr21:44401681, elapsed 0.1s, est remaining 0.4s, peak mem 127MB, user 0.5s, sys 0.0s, output queue size 69
progress 20% @chr21:44533685, elapsed 0.1s, est remaining 0.3s, peak mem 133MB, user 0.6s, sys 0.0s, output queue size 99
progress 25% @chr21:44550691, elapsed 0.3s, est remaining 1.0s, peak mem 221MB, user 1.0s, sys 0.0s, output queue size 108
progress 34% @chr21:44224713, elapsed 0.5s, est remaining 0.9s, peak mem 232MB, user 2.4s, sys 0.0s, output queue size 115
progress 35% @chr21:44637418, elapsed 0.5s, est remaining 0.9s, peak mem 233MB, user 2.8s, sys 0.0s, output queue size 9
progress 40% @chr21:44813862, elapsed 0.5s, est remaining 0.7s, peak mem 233MB, user 4.3s, sys 0.0s, output queue size 21
progress 45% @chr21:44539302, elapsed 0.5s, est remaining 0.6s, peak mem 233MB, user 5.3s, sys 0.0s, output queue size 45
progress 50% @chr21:45267451, elapsed 0.5s, est remaining 0.5s, peak mem 235MB, user 5.8s, sys 0.0s, output queue size 11
progress 55% @chr21:45455531, elapsed 0.5s, est remaining 0.4s, peak mem 235MB, user 5.9s, sys 0.0s, output queue size 21
progress 60% @chr21:45913951, elapsed 0.5s, est remaining 0.4s, peak mem 235MB, user 6.0s, sys 0.0s, output queue size 22
progress 65% @chr21:46002218, elapsed 0.6s, est remaining 0.3s, peak mem 235MB, user 6.3s, sys 0.0s, output queue size 14
progress 70% @chr21:46131954, elapsed 0.6s, est remaining 0.3s, peak mem 238MB, user 6.5s, sys 0.0s, output queue size 51
progress 75% @chr21:46270401, elapsed 0.6s, est remaining 0.2s, peak mem 238MB, user 6.6s, sys 0.0s, output queue size 82
progress 80% @chr21:46125785, elapsed 0.7s, est remaining 0.2s, peak mem 238MB, user 7.1s, sys 0.0s, output queue size 83
progress 85% @chr21:46399590, elapsed 0.7s, est remaining 0.1s, peak mem 238MB, user 7.1s, sys 0.0s, output queue size 15
progress 90% @chr21:46440855, elapsed 0.8s, est remaining 0.1s, peak mem 238MB, user 7.2s, sys 0.0s, output queue size 35
progress 95% @chr21:46550543, elapsed 0.8s, est remaining 0.0s, peak mem 238MB, user 7.6s, sys 0.0s, output queue size 19
progress 100% @chr21:46660833, elapsed 0.8s, est remaining 0.0s, peak mem 238MB, user 7.7s, sys 0.1s, output queue size 3
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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 208827488
output file size: 38078
reads: 2481283
contig: 516 intervals 92221 bases
"assemble": 89 calls 0.201 user 0.000 sys 0.334 real
"assemble_addRead": 89 calls 0.000 user 0.000 sys 0.015 real
"assemble_buildGraph": 199 calls 0.110 user 0.000 sys 0.174 real
"assemble_computecigar": 129 calls 0.177 user 0.006 sys 0.223 real
"assemble_kg_build_calcsize": 199 calls 0.046 user 0.000 sys 0.107 real
"assemble_kg_build_clear": 260 calls 0.013 user 0.000 sys 0.008 real
"assemble_kg_build_prepare": 398 calls 0.027 user 0.000 sys 0.082 real
"assemble_kg_build_threading": 138 calls 0.064 user 0.000 sys 0.063 real
"assemble_kg_op1": 138 calls 0.023 user 0.000 sys 0.015 real
"assemble_kg_op2": 138 calls 0.000 user 0.000 sys 0.005 real
"assemble_kg_op3": 138 calls 0.000 user 0.000 sys 0.004 real
"assemble_sg_clean": 129 calls 0.020 user 0.000 sys 0.014 real
"assemble_sg_create": 129 calls 0.008 user 0.000 sys 0.016 real
"checkGraph": 89 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 89 calls 0.177 user 0.006 sys 0.232 real
active: 1044 calls 0.000 user 0.000 sys 0.004 real
advance: 528 calls 1.715 user 0.037 sys 1.893 real
annotate: 116 calls 0.003 user 0.000 sys 0.013 real
assemble_region: 89 calls 0.378 user 0.006 sys 0.581 real
build_variants: 88 calls 0.000 user 0.000 sys 0.001 real
calc: 1044 calls 0.123 user 0.000 sys 0.180 real
calc_region: 88 calls 3.465 user 0.001 sys 3.498 real
call_region: 88 calls 0.023 user 0.000 sys 0.024 real
clip_region: 177 calls 0.000 user 0.000 sys 0.027 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.009 user 0.000 sys 0.780 real
fetch: 1044 calls 0.073 user 0.000 sys 0.078 real
fetch_db: 88 calls 0.000 user 0.000 sys 0.028 real
fetch_ref: 1133 calls 0.029 user 0.000 sys 0.005 real
fetch_region: 89 calls 0.020 user 0.000 sys 0.007 real
idle: 41 calls 0.040 user 0.000 sys 12.412 real
init: 1 calls 0.040 user 0.000 sys 0.041 real
pairhmm: 815 calls 5.637 user 0.004 sys 5.890 real
realign: 246 calls 0.250 user 0.000 sys 0.312 real
region: 1044 calls 5.683 user 0.013 sys 5.727 real
tracker: 1044 calls 0.000 user 0.000 sys 0.004 real
trim_region: 89 calls 0.010 user 0.000 sys 0.003 real
overall: 249921536 mem 9.149 user 0.081 sys 1.880 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory