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/4a/1ed9c330d3210e2333699062116a6f/.command.sh
  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/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/a4798a32f5e9daf45b045790a1d26d/HCC1395_BL.recalibrated.bam.bai
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr4_30730753-30730788.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/1ed9c330d3210e2333699062116a6f/.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 chr4_30730753-30730788.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86774373, elapsed 0.0s, est remaining 0.8s, peak mem 84MB, user 0.1s, sys 0.1s, output queue size 2158
progress 10% @chr4:152643088, elapsed 0.1s, est remaining 0.7s, peak mem 94MB, user 0.1s, sys 0.2s, output queue size 4580
progress 15% @chr5:36170344, elapsed 0.1s, est remaining 0.6s, peak mem 105MB, user 0.1s, sys 0.3s, output queue size 7024
progress 20% @chr5:91072447, elapsed 0.2s, est remaining 0.6s, peak mem 114MB, user 0.1s, sys 0.4s, output queue size 1713
progress 25% @chr5:141192553, elapsed 0.2s, est remaining 0.6s, peak mem 123MB, user 0.1s, sys 0.6s, output queue size 4117
progress 30% @chr5:177293824, elapsed 0.2s, est remaining 0.5s, peak mem 133MB, user 0.2s, sys 0.7s, output queue size 6235
progress 35% @chr6:30948547, elapsed 0.3s, est remaining 0.5s, peak mem 142MB, user 0.2s, sys 0.8s, output queue size 8426
progress 40% @chr6:43675494, elapsed 0.3s, est remaining 0.5s, peak mem 153MB, user 0.2s, sys 1.0s, output queue size 10980
progress 45% @chr6:106519131, elapsed 0.3s, est remaining 0.4s, peak mem 163MB, user 0.3s, sys 1.1s, output queue size 13436
progress 50% @chr6:149450683, elapsed 0.4s, est remaining 0.4s, peak mem 171MB, user 0.3s, sys 1.3s, output queue size 15531
progress 55% @chr7:13911239, elapsed 0.4s, est remaining 0.3s, peak mem 178MB, user 0.3s, sys 1.5s, output queue size 17789
progress 60% @chr7:64077276, elapsed 0.4s, est remaining 0.3s, peak mem 189MB, user 0.3s, sys 1.6s, output queue size 19863
progress 65% @chr7:100951841, elapsed 0.5s, est remaining 0.3s, peak mem 199MB, user 0.3s, sys 1.8s, output queue size 22380
progress 70% @chr7:139345501, elapsed 0.5s, est remaining 0.2s, peak mem 210MB, user 0.4s, sys 1.9s, output queue size 24743
progress 75% @chr8:13099347, elapsed 0.6s, est remaining 0.2s, peak mem 220MB, user 0.4s, sys 2.0s, output queue size 26807
progress 80% @chr8:38840224, elapsed 0.6s, est remaining 0.1s, peak mem 226MB, user 0.4s, sys 2.2s, output queue size 28426
progress 85% @chrX:15511437, elapsed 0.6s, est remaining 0.1s, peak mem 235MB, user 0.4s, sys 2.3s, output queue size 30933
progress 90% @chrX:54951905, elapsed 0.7s, est remaining 0.1s, peak mem 246MB, user 0.4s, sys 2.4s, output queue size 33297
progress 95% @chrX:111721603, elapsed 0.7s, est remaining 0.0s, peak mem 253MB, user 0.5s, sys 2.5s, output queue size 35233
progress 100% @chrX:154310836, elapsed 0.7s, est remaining 0.0s, peak mem 265MB, user 0.5s, sys 2.6s, output queue size 37451
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.83
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: 71692772
output file size: 22309
reads: 1001089
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.001 user 0.001 sys 0.000 real
"assemble_addRead": 1 calls 0.000 user 0.000 sys 0.000 real
"assemble_buildGraph": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_computecigar": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_calcsize": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_clear": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_prepare": 4 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_build_threading": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op1": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op2": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_kg_op3": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_clean": 2 calls 0.000 user 0.000 sys 0.000 real
"assemble_sg_create": 2 calls 0.001 user 0.001 sys 0.000 real
"checkGraph": 1 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 1 calls 0.000 user 0.000 sys 0.000 real
active: 93348 calls 0.010 user 0.010 sys 0.020 real
advance: 47638 calls 0.009 user 0.011 sys 0.026 real
assemble_region: 1 calls 0.001 user 0.001 sys 0.000 real
calc: 93348 calls 0.000 user 0.000 sys 0.020 real
clip_region: 1 calls 0.000 user 0.000 sys 0.000 real
done: 1 calls 0.000 user 0.000 sys 0.002 real
execute: 1 calls 0.004 user 0.000 sys 1.302 real
fetch: 93348 calls 0.000 user 0.003 sys 0.021 real
fetch_ref: 93349 calls 0.060 user 0.067 sys 0.348 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 39 calls 0.005 user 0.015 sys 19.198 real
init: 1 calls 0.039 user 0.001 sys 0.041 real
region: 93348 calls 0.000 user 0.021 sys 0.023 real
tracker: 93348 calls 0.041 user 0.020 sys 0.089 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 281821184 mem 1.153 user 4.867 sys 2.416 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory