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/e7/493cf948b1d450f8051fba2ea0097a/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/30/cd7a71c824521b52d5298cf6761d93/.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/e7/493cf948b1d450f8051fba2ea0097a/HCC1395_BL.recalibrated.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/cd7a71c824521b52d5298cf6761d93/.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% @chr1:113710154, elapsed 0.7s, est remaining 12.6s, peak mem 145MB, user 6.8s, sys 0.5s, output queue size 4
progress 10% @chr2:3643344, elapsed 1.3s, est remaining 11.7s, peak mem 145MB, user 13.2s, sys 0.9s, output queue size 6
progress 15% @chr2:178606921, elapsed 2.0s, est remaining 11.1s, peak mem 145MB, user 20.0s, sys 1.3s, output queue size 11
progress 20% @chr3:57483276, elapsed 2.6s, est remaining 10.3s, peak mem 145MB, user 26.2s, sys 1.7s, output queue size 0
progress 25% @chr4:70603777, elapsed 3.2s, est remaining 9.7s, peak mem 145MB, user 33.0s, sys 2.1s, output queue size 8
progress 30% @chr5:135873921, elapsed 3.9s, est remaining 9.1s, peak mem 147MB, user 39.8s, sys 2.6s, output queue size 4
progress 35% @chr6:104957999, elapsed 4.5s, est remaining 8.4s, peak mem 148MB, user 46.1s, sys 2.9s, output queue size 3
progress 40% @chr7:106882933, elapsed 5.2s, est remaining 7.8s, peak mem 149MB, user 52.9s, sys 3.2s, output queue size 2
progress 45% @chr8:143821497, elapsed 5.8s, est remaining 7.1s, peak mem 150MB, user 59.8s, sys 3.6s, output queue size 1
progress 50% @chr10:21726144, elapsed 6.5s, est remaining 6.5s, peak mem 152MB, user 66.2s, sys 4.1s, output queue size 2
progress 55% @chr11:34132926, elapsed 7.1s, est remaining 5.8s, peak mem 152MB, user 72.8s, sys 4.4s, output queue size 3
progress 60% @chr12:12718707, elapsed 7.7s, est remaining 5.2s, peak mem 154MB, user 79.1s, sys 4.7s, output queue size 10
progress 65% @chr13:32149648, elapsed 8.4s, est remaining 4.5s, peak mem 154MB, user 85.7s, sys 5.2s, output queue size 0
progress 70% @chr15:35521993, elapsed 9.0s, est remaining 3.9s, peak mem 155MB, user 92.1s, sys 5.5s, output queue size 3
progress 75% @chr16:28494582, elapsed 9.6s, est remaining 3.2s, peak mem 155MB, user 98.6s, sys 5.9s, output queue size 0
progress 80% @chr17:40034816, elapsed 10.3s, est remaining 2.6s, peak mem 155MB, user 105.8s, sys 6.3s, output queue size 1
progress 85% @chr19:1806528, elapsed 11.0s, est remaining 1.9s, peak mem 155MB, user 112.6s, sys 6.7s, output queue size 3
progress 90% @chr19:54630974, elapsed 11.6s, est remaining 1.3s, peak mem 155MB, user 119.3s, sys 7.0s, output queue size 2
progress 95% @chr22:31897382, elapsed 13.1s, est remaining 0.7s, peak mem 333MB, user 134.4s, sys 7.5s, output queue size 10
progress 100% @chr6_GL000251v2_alt:3938900, elapsed 13.7s, est remaining 0.0s, peak mem 333MB, user 140.6s, sys 7.9s, output queue size 427
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 71692765
output file size: 46614
reads: 1501772
contig: 178193 intervals 76355618 bases
"assemble": 183 calls 0.409 user 0.020 sys 0.406 real
"assemble_addRead": 183 calls 0.000 user 0.000 sys 0.007 real
"assemble_buildGraph": 422 calls 0.198 user 0.001 sys 0.172 real
"assemble_computecigar": 264 calls 0.070 user 0.010 sys 0.073 real
"assemble_kg_build_calcsize": 422 calls 0.086 user 0.000 sys 0.088 real
"assemble_kg_build_clear": 573 calls 0.020 user 0.000 sys 0.007 real
"assemble_kg_build_prepare": 844 calls 0.039 user 0.020 sys 0.085 real
"assemble_kg_build_threading": 271 calls 0.107 user 0.001 sys 0.080 real
"assemble_kg_op1": 271 calls 0.037 user 0.000 sys 0.056 real
"assemble_kg_op2": 271 calls 0.000 user 0.000 sys 0.004 real
"assemble_kg_op3": 271 calls 0.010 user 0.000 sys 0.005 real
"assemble_sg_clean": 264 calls 0.020 user 0.000 sys 0.020 real
"assemble_sg_create": 264 calls 0.060 user 0.000 sys 0.031 real
"checkGraph": 183 calls 0.000 user 0.000 sys 0.000 real
"findHaplotype": 183 calls 0.080 user 0.010 sys 0.077 real
advance: 189104 calls 15.254 user 0.331 sys 18.638 real
assemble_region: 183 calls 0.489 user 0.038 sys 0.491 real
build_pileup: 70974 calls 0.377 user 0.033 sys 0.460 real
build_stats: 71688 calls 2.154 user 0.058 sys 2.265 real
build_variants: 142 calls 0.000 user 0.000 sys 0.001 real
calc: 128670 calls 2.343 user 0.048 sys 2.955 real
calc_region: 142 calls 2.225 user 0.029 sys 2.285 real
call_region: 142 calls 0.039 user 0.000 sys 0.038 real
clip_region: 325 calls 0.000 user 0.000 sys 0.028 real
done: 1 calls 0.454 user 0.000 sys 0.460 real
execute: 1 calls 0.006 user 0.002 sys 13.722 real
fetch: 743546 calls 0.646 user 0.037 sys 0.849 real
fetch_ref: 745688 calls 1.622 user 0.478 sys 2.723 real
fetch_region: 183 calls 0.010 user 0.000 sys 0.007 real
fetch_vcf: 189104 calls 43.837 user 0.773 sys 55.965 real
idle: 35 calls 0.003 user 0.000 sys 12.863 real
init: 1 calls 0.040 user 0.010 sys 0.058 real
pairhmm: 472 calls 3.297 user 0.028 sys 3.423 real
realign: 142 calls 0.351 user 0.000 sys 0.343 real
region: 367297 calls 2.735 user 0.081 sys 2.880 real
tracker: 367297 calls 0.434 user 0.061 sys 0.557 real
trim_region: 183 calls 0.000 user 0.000 sys 0.002 real
overall: 350072832 mem 156.553 user 10.648 sys 15.034 real