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/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/9224b114c369a1a447550d5fcd91e5/.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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/beta/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
Downloading: s3://natera-platform-sandbox/pipeline-resources/beds/altera_subpanels/hg38/foresight/xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/9224b114c369a1a447550d5fcd91e5/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/Sig_18_Blood.md.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4c/f84457a21aa906d2a86c8a3c95aa99/Sig_18_Blood.md.bam.bai
Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
==> STAGING COMPLETE (13 inputs)
cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_Blood.md.bam --interval xgen-exome-hyb-panel-v2-targets-hg38_AND_altera_v3_targets_postQC_hg38_AND_foresight_clarity.bed --algo QualCal -k dbsnp_146.hg38.vcf.gz -k Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -k Homo_sapiens_assembly38.known_indels.vcf.gz Sig_18_Blood.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119893964, elapsed 0.1s, est remaining 1.0s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 578
progress 10% @chr2:17931009, elapsed 0.1s, est remaining 0.9s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 246
progress 15% @chr2:189039272, elapsed 0.2s, est remaining 0.9s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 124
progress 20% @chr3:97942284, elapsed 0.2s, est remaining 0.8s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 105
progress 25% @chr4:88521888, elapsed 0.3s, est remaining 0.8s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 5095
progress 30% @chr5:146514854, elapsed 0.3s, est remaining 0.7s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 905
progress 35% @chr6:127137390, elapsed 0.3s, est remaining 0.6s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 10848
progress 40% @chr7:128807360, elapsed 0.4s, est remaining 0.6s, peak mem 160MB, user 0.0s, sys 0.0s, output queue size 2249
progress 45% @chr9:429702, elapsed 0.4s, est remaining 0.5s, peak mem 277MB, user 0.0s, sys 0.1s, output queue size 11615
progress 50% @chr10:32635057, elapsed 0.5s, est remaining 0.5s, peak mem 286MB, user 0.0s, sys 0.1s, output queue size 21561
progress 55% @chr11:48245104, elapsed 0.5s, est remaining 0.4s, peak mem 295MB, user 0.0s, sys 0.1s, output queue size 32021
progress 60% @chr12:22046304, elapsed 0.6s, est remaining 0.4s, peak mem 298MB, user 0.0s, sys 0.1s, output queue size 7759
progress 65% @chr13:49220338, elapsed 0.6s, est remaining 0.3s, peak mem 298MB, user 0.0s, sys 0.1s, output queue size 18808
progress 70% @chr15:42718752, elapsed 0.7s, est remaining 0.3s, peak mem 298MB, user 0.0s, sys 0.1s, output queue size 28847
progress 75% @chr16:30964094, elapsed 0.7s, est remaining 0.2s, peak mem 298MB, user 0.0s, sys 0.1s, output queue size 38422
progress 80% @chr17:42422627, elapsed 0.8s, est remaining 0.2s, peak mem 298MB, user 0.0s, sys 0.1s, output queue size 49103
progress 85% @chr19:5641740, elapsed 0.8s, est remaining 0.1s, peak mem 325MB, user 0.0s, sys 0.1s, output queue size 59511
progress 90% @chr19:55716728, elapsed 0.9s, est remaining 0.1s, peak mem 325MB, user 0.0s, sys 0.1s, output queue size 69009
progress 95% @chr22:36937342, elapsed 1.3s, est remaining 0.1s, peak mem 2491MB, user 6.2s, sys 2.7s, output queue size 3223
progress 100% @chrY:57184264, elapsed 1.3s, est remaining 0.0s, peak mem 2491MB, user 6.3s, sys 2.7s, output queue size 5376
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: 31 max 384
algo: QualCal
license: sentieon:QualCal=31
input file size: 52290600
reads: 1001133
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.847 user 0.099 sys 2.273 real
done: 1 calls 0.285 user 0.138 sys 0.424 real
execute: 1 calls 0.011 user 0.000 sys 1.331 real
fetch_reads: 208647 calls 0.056 user 0.000 sys 0.174 real
fetch_ref: 2072 calls 0.002 user 0.005 sys 0.023 real
fetch_vcf: 2072 calls 0.825 user 0.046 sys 0.972 real
idle: 92 calls 0.004 user 0.001 sys 31.816 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2257 calls 4.518 user 2.558 sys 7.677 real
overall: 2612486144 mem 10.517 user 9.403 sys 2.706 real
ls: cannot access '*.table.post': No such file or directory
ls: cannot access '*.recalibrated.bam': No such file or directory
ls: cannot access '*.recalibrated.bam.bai': No such file or directory
ls: cannot access '*.csv': No such file or directory
ls: cannot access '*.pdf': No such file or directory