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/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/28/9b07206464e732a00b7bf74852ddd6/HCC1395_BL.recalibrated.bam
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/dna_daq/stored-normals/reference-NA12878-downsampled-500k.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_padded_intervals/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/.command.sh
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/PON/pon_tnseq_42_curated_v4.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/28/9b07206464e732a00b7bf74852ddd6/HCC1395_BL.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/d0c388585784c28bb45e081d415454/.command.run
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
==> STAGING COMPLETE (14 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 12 -r Homo_sapiens_assembly38.fasta -i reference-NA12878-downsampled-500k.bam -i HCC1395_BL.recalibrated.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity_padded100bp.bed --algo TNhaplotyper2 --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --call_germline_sites --germline_vcf af-only-gnomad.hg38.vcf.gz --pon pon_tnseq_42_curated_v4.vcf.gz negative_somatic_control_1.tnseq.vcf.gz --algo OrientationBias --tumor_sample HCC1395_BL negative_somatic_control_1.tnseq.orientation_data.tsv --algo ContaminationModel --tumor_sample HCC1395_BL --normal_sample reference-NA12878 --vcf af-only-gnomad.hg38.vcf.gz --tumor_segments negative_somatic_control_1.tnseq.segments negative_somatic_control_1.tnseq.contamination_data.tsv
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:113682797, elapsed 0.7s, est remaining 12.9s, peak mem 145MB, user 6.7s, sys 0.5s, output queue size 3
progress 10% @chr2:3671058, elapsed 1.3s, est remaining 11.7s, peak mem 145MB, user 13.2s, sys 0.8s, output queue size 5
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 20.1s, sys 1.1s, output queue size 12
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 146MB, user 26.1s, sys 1.6s, output queue size 0
progress 25% @chr4:70598256, elapsed 3.2s, est remaining 9.7s, peak mem 146MB, user 32.9s, sys 2.0s, output queue size 3
progress 30% @chr5:135571753, elapsed 3.9s, est remaining 9.1s, peak mem 148MB, user 39.7s, sys 2.3s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.3s, peak mem 149MB, user 45.9s, sys 2.6s, output queue size 2
progress 40% @chr7:106872437, elapsed 5.1s, est remaining 7.7s, peak mem 150MB, user 52.7s, sys 3.0s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 151MB, user 59.3s, sys 3.4s, output queue size 0
progress 50% @chr10:21727756, elapsed 6.4s, est remaining 6.4s, peak mem 152MB, user 65.7s, sys 3.8s, output queue size 2
progress 55% @chr11:34132025, elapsed 7.1s, est remaining 5.8s, peak mem 153MB, user 72.2s, sys 4.2s, output queue size 2
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.1s, peak mem 153MB, user 78.2s, sys 4.6s, output queue size 11
progress 65% @chr13:32078734, elapsed 8.3s, est remaining 4.5s, peak mem 153MB, user 84.9s, sys 5.0s, output queue size 10
progress 70% @chr15:35381722, elapsed 8.9s, est remaining 3.8s, peak mem 153MB, user 91.2s, sys 5.4s, output queue size 2
progress 75% @chr16:28489190, elapsed 9.6s, est remaining 3.2s, peak mem 154MB, user 97.5s, sys 5.8s, output queue size 1
progress 80% @chr17:40034816, elapsed 10.3s, est remaining 2.6s, peak mem 154MB, user 104.8s, sys 6.2s, output queue size 0
progress 85% @chr19:1805788, elapsed 10.9s, est remaining 1.9s, peak mem 154MB, user 111.4s, sys 6.7s, output queue size 3
progress 90% @chr19:54632916, elapsed 11.5s, est remaining 1.3s, peak mem 154MB, user 117.9s, sys 7.2s, output queue size 0
progress 95% @chr22:31944634, elapsed 13.0s, est remaining 0.7s, peak mem 318MB, user 132.8s, sys 7.6s, output queue size 10
progress 100% @chrY:20768705, elapsed 13.6s, est remaining 0.0s, peak mem 318MB, user 138.8s, sys 8.1s, output queue size 204
sw version: sentieon-genomics-202308.03
os version: Linux 6.12.88
cpu vendor: GenuineIntel
signature: 000606a6
features: 1f8bfbff fffa320b
extended: f1bf07ab 00407f5a
amd bits: 2c100800 00000121
brand: Intel(R) Xeon(R) Platinum 8375C CPU @ 2.90GHz
threads: 12 max 64
algo: TNhaplotyper2 OrientationBias ContaminationModel
license: sentieon:TNhaplotyper=12
input file size: 71721858 71692773
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.358 user 0.001 sys 0.393 real
"assemble_addRead": 183 calls 0.010 user 0.000 sys 0.006 real
"assemble_buildGraph": 422 calls 0.136 user 0.000 sys 0.167 real
"assemble_computecigar": 264 calls 0.041 user 0.019 sys 0.068 real
"assemble_kg_build_calcsize": 422 calls 0.054 user 0.000 sys 0.086 real
"assemble_kg_build_clear": 573 calls 0.000 user 0.000 sys 0.006 real
"assemble_kg_build_prepare": 844 calls 0.135 user 0.000 sys 0.082 real
"assemble_kg_build_threading": 271 calls 0.081 user 0.000 sys 0.077 real
"assemble_kg_op1": 271 calls 0.039 user 0.001 sys 0.055 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 271 calls 0.000 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.000 user 0.000 sys 0.020 real
"assemble_sg_create": 264 calls 0.038 user 0.000 sys 0.030 real
"checkGraph": 183 calls 0.010 user 0.000 sys 0.000 real
"findHaplotype": 183 calls 0.041 user 0.019 sys 0.071 real
advance: 189104 calls 15.173 user 0.390 sys 18.480 real
assemble_region: 183 calls 0.419 user 0.020 sys 0.472 real
build_pileup: 70974 calls 0.380 user 0.009 sys 0.449 real
build_stats: 71688 calls 1.976 user 0.040 sys 2.164 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.122 user 0.051 sys 2.861 real
calc_region: 142 calls 2.341 user 0.012 sys 2.350 real
call_region: 142 calls 0.058 user 0.000 sys 0.037 real
clip_region: 325 calls 0.020 user 0.000 sys 0.026 real
done: 1 calls 0.433 user 0.009 sys 0.445 real
execute: 1 calls 0.007 user 0.002 sys 13.624 real
fetch: 743546 calls 0.639 user 0.067 sys 0.814 real
fetch_ref: 745688 calls 1.622 user 0.472 sys 2.707 real
fetch_region: 183 calls 0.000 user 0.000 sys 0.006 real
fetch_vcf: 189104 calls 42.381 user 0.789 sys 55.386 real
idle: 35 calls 0.003 user 0.012 sys 12.804 real
init: 1 calls 0.050 user 0.000 sys 0.058 real
pairhmm: 472 calls 3.417 user 0.010 sys 3.369 real
realign: 142 calls 0.277 user 0.000 sys 0.340 real
region: 367297 calls 2.761 user 0.084 sys 2.924 real
tracker: 367297 calls 0.492 user 0.056 sys 0.541 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 333848576 mem 154.238 user 11.000 sys 14.919 real