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-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/3b/5ee99cf72c5eedce7d38635e9e9369/.command.sh
  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/3b/5ee99cf72c5eedce7d38635e9e9369/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/Sig_18_Blood.recalibrated.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/16/fd07f3bccb2b3e7b5521fe26c79365/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 chr4_30730753-30730788.bed.gz -i Sig_18_Blood.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_2.haplotyper.chr4_30730753-30730788.bed.unfiltered.vcf.gz
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr4:86803709, elapsed 0.1s, est remaining 1.3s, peak mem 75MB, user 0.0s, sys 0.3s, output queue size 2296
progress 10% @chr4:152332564, elapsed 0.1s, est remaining 1.2s, peak mem 75MB, user 0.1s, sys 0.6s, output queue size 1116
progress 15% @chr5:36163645, elapsed 0.2s, est remaining 1.1s, peak mem 87MB, user 0.1s, sys 0.8s, output queue size 3588
progress 20% @chr5:91072447, elapsed 0.3s, est remaining 1.1s, peak mem 96MB, user 0.1s, sys 1.1s, output queue size 6169
progress 25% @chr5:141192553, elapsed 0.3s, est remaining 1.0s, peak mem 108MB, user 0.1s, sys 1.4s, output queue size 8570
progress 30% @chr5:177302752, elapsed 0.4s, est remaining 0.9s, peak mem 120MB, user 0.2s, sys 1.6s, output queue size 10689
progress 35% @chr6:30948547, elapsed 0.4s, est remaining 0.8s, peak mem 129MB, user 0.2s, sys 2.0s, output queue size 12880
progress 40% @chr6:43774579, elapsed 0.5s, est remaining 0.8s, peak mem 135MB, user 0.3s, sys 2.3s, output queue size 15445
progress 45% @chr6:106519131, elapsed 0.6s, est remaining 0.7s, peak mem 144MB, user 0.3s, sys 2.7s, output queue size 17887
progress 50% @chr6:149450683, elapsed 0.7s, est remaining 0.7s, peak mem 147MB, user 0.3s, sys 2.9s, output queue size 19987
progress 55% @chr7:13911239, elapsed 0.7s, est remaining 0.6s, peak mem 162MB, user 0.4s, sys 3.2s, output queue size 22245
progress 60% @chr7:64219314, elapsed 0.8s, est remaining 0.5s, peak mem 168MB, user 0.4s, sys 3.5s, output queue size 24316
progress 65% @chr7:100951841, elapsed 0.9s, est remaining 0.5s, peak mem 177MB, user 0.4s, sys 3.8s, output queue size 26838
progress 70% @chr7:139283024, elapsed 0.9s, est remaining 0.4s, peak mem 186MB, user 0.4s, sys 4.2s, output queue size 29200
progress 75% @chr8:13115586, elapsed 1.0s, est remaining 0.3s, peak mem 192MB, user 0.5s, sys 4.6s, output queue size 31261
progress 80% @chr8:38976535, elapsed 1.0s, est remaining 0.3s, peak mem 198MB, user 0.5s, sys 4.8s, output queue size 32905
progress 85% @chrX:15491162, elapsed 1.1s, est remaining 0.2s, peak mem 207MB, user 0.5s, sys 5.1s, output queue size 35388
progress 90% @chrX:55002251, elapsed 1.2s, est remaining 0.1s, peak mem 213MB, user 0.5s, sys 5.5s, output queue size 37755
progress 95% @chrX:111712484, elapsed 1.2s, est remaining 0.1s, peak mem 222MB, user 0.6s, sys 5.7s, output queue size 39685
progress 100% @chrX:154965970, elapsed 1.3s, est remaining 0.0s, peak mem 231MB, user 0.6s, sys 6.0s, output queue size 41907
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 384
algo: Haplotyper
license: sentieon:Haplotyper=12
input file size: 74586815
output file size: 22311
reads: 1001133
contig: 45710 intervals 9000068 bases
"assemble": 1 calls 0.000 user 0.000 sys 0.001 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 0.000 user 0.000 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 0.000 user 0.006 sys 0.017 real
advance: 47638 calls 0.001 user 0.009 sys 0.027 real
assemble_region: 1 calls 0.000 user 0.000 sys 0.001 real
calc: 93348 calls 0.000 user 0.000 sys 0.017 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 0.003 sys 2.905 real
fetch: 93348 calls 0.011 user 0.000 sys 0.018 real
fetch_ref: 93349 calls 0.078 user 0.112 sys 0.428 real
fetch_region: 1 calls 0.000 user 0.000 sys 0.000 real
idle: 51 calls 0.003 user 0.010 sys 32.007 real
init: 1 calls 0.020 user 0.020 sys 0.042 real
region: 93348 calls 0.009 user 0.001 sys 0.024 real
tracker: 93348 calls 0.036 user 0.003 sys 0.086 real
trim_region: 1 calls 0.000 user 0.000 sys 0.000 real
overall: 245501952 mem 1.283 user 9.535 sys 4.031 real
ls: cannot access '*.g.vcf.gz': No such file or directory
ls: cannot access '*.g.vcf.gz.tbi': No such file or directory