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/1d/a97921250fae941e04393d263c5eb3/.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/1d/a97921250fae941e04393d263c5eb3/.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 0.2s, peak mem 79MB, user 0.0s, sys 0.0s, output queue size 1
progress 10% @chr21:44286007, elapsed 0.0s, est remaining 0.4s, peak mem 100MB, user 0.2s, sys 0.0s, output queue size 39
progress 15% @chr21:44401681, elapsed 0.1s, est remaining 0.3s, peak mem 121MB, user 0.4s, sys 0.0s, output queue size 71
progress 20% @chr21:44437062, elapsed 0.1s, est remaining 0.2s, peak mem 123MB, user 0.4s, sys 0.0s, output queue size 88
progress 25% @chr21:44550691, elapsed 0.1s, est remaining 0.2s, peak mem 135MB, user 0.5s, sys 0.0s, output queue size 108
progress 34% @chr21:44224713, elapsed 0.2s, est remaining 0.4s, peak mem 206MB, user 0.9s, sys 0.1s, output queue size 113
progress 35% @chr21:44697202, elapsed 0.2s, est remaining 0.4s, peak mem 208MB, user 0.9s, sys 0.1s, output queue size 7
progress 40% @chr21:44873502, elapsed 0.2s, est remaining 0.3s, peak mem 208MB, user 1.5s, sys 0.1s, output queue size 27
progress 45% @chr21:44967034, elapsed 0.2s, est remaining 0.3s, peak mem 208MB, user 1.9s, sys 0.1s, output queue size 48
progress 50% @chr21:44637418, elapsed 0.3s, est remaining 0.3s, peak mem 208MB, user 2.2s, sys 0.1s, output queue size 70
progress 55% @chr21:45491225, elapsed 0.3s, est remaining 0.2s, peak mem 208MB, user 2.4s, sys 0.1s, output queue size 26
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progress 65% @chr21:46122875, elapsed 0.3s, est remaining 0.2s, peak mem 208MB, user 2.8s, sys 0.2s, output queue size 17
progress 70% @chr21:46168308, elapsed 0.3s, est remaining 0.1s, peak mem 209MB, user 2.9s, sys 0.2s, output queue size 24
progress 75% @chr21:46258939, elapsed 0.4s, est remaining 0.1s, peak mem 209MB, user 3.0s, sys 0.2s, output queue size 53
progress 80% @chr21:46326377, elapsed 0.4s, est remaining 0.1s, peak mem 209MB, user 3.4s, sys 0.2s, output queue size 11
progress 85% @chr21:46391164, elapsed 0.4s, est remaining 0.1s, peak mem 209MB, user 3.6s, sys 0.2s, output queue size 36
progress 90% @chr21:46430010, elapsed 0.4s, est remaining 0.0s, peak mem 209MB, user 3.7s, sys 0.2s, output queue size 25
progress 95% @chr21:46554575, elapsed 0.4s, est remaining 0.0s, peak mem 209MB, user 3.8s, sys 0.2s, output queue size 32
progress 100% @chr21:46602278, elapsed 0.4s, est remaining 0.0s, peak mem 209MB, user 3.9s, sys 0.2s, 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 192
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 163002590
output file size: 38710
reads: 1955548
contig: 516 intervals 92221 bases
"assemble": 96 calls 0.154 user 0.008 sys 0.224 real
"assemble_addRead": 96 calls 0.010 user 0.000 sys 0.010 real
"assemble_buildGraph": 205 calls 0.064 user 0.000 sys 0.113 real
"assemble_computecigar": 140 calls 0.065 user 0.006 sys 0.144 real
"assemble_kg_build_calcsize": 205 calls 0.040 user 0.000 sys 0.067 real
"assemble_kg_build_clear": 265 calls 0.001 user 0.000 sys 0.004 real
"assemble_kg_build_prepare": 410 calls 0.048 user 0.008 sys 0.052 real
"assemble_kg_build_threading": 145 calls 0.023 user 0.000 sys 0.044 real
"assemble_kg_op1": 145 calls 0.006 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 0.014 user 0.000 sys 0.012 real
"assemble_sg_create": 140 calls 0.003 user 0.000 sys 0.015 real
"checkGraph": 96 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 96 calls 0.065 user 0.006 sys 0.148 real
active: 1044 calls 0.000 user 0.000 sys 0.003 real
advance: 528 calls 1.110 user 0.092 sys 1.415 real
annotate: 105 calls 0.000 user 0.000 sys 0.009 real
assemble_region: 96 calls 0.229 user 0.014 sys 0.384 real
build_variants: 95 calls 0.000 user 0.000 sys 0.000 real
calc: 1044 calls 0.112 user 0.000 sys 0.126 real
calc_region: 95 calls 1.339 user 0.018 sys 1.515 real
call_region: 95 calls 0.011 user 0.000 sys 0.016 real
clip_region: 191 calls 0.007 user 0.004 sys 0.018 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.004 sys 0.450 real
fetch: 1044 calls 0.052 user 0.000 sys 0.058 real
fetch_db: 95 calls 0.035 user 0.000 sys 0.030 real
fetch_ref: 1140 calls 0.004 user 0.000 sys 0.005 real
fetch_region: 96 calls 0.008 user 0.000 sys 0.005 real
idle: 54 calls 0.057 user 0.000 sys 12.530 real
init: 1 calls 0.018 user 0.019 sys 0.042 real
pairhmm: 430 calls 2.388 user 0.056 sys 2.784 real
realign: 197 calls 0.163 user 0.003 sys 0.172 real
region: 1044 calls 2.562 user 0.061 sys 2.708 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: 221413376 mem 4.926 user 0.283 sys 1.554 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory