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/e5/5e14d3c54516fce231a15f3d7307d2/HCC1395_BL.md.bam
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/7f/f5e082a230a78092275a6a1565f0e7/.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/7f/f5e082a230a78092275a6a1565f0e7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e5/5e14d3c54516fce231a15f3d7307d2/HCC1395_BL.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 HCC1395_BL.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 HCC1395_BL.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119834765, elapsed 0.0s, est remaining 0.9s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 1116
progress 10% @chr2:17785862, elapsed 0.1s, est remaining 0.8s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 5353
progress 15% @chr2:189053895, elapsed 0.1s, est remaining 0.8s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 399
progress 20% @chr3:97899137, elapsed 0.2s, est remaining 0.7s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 10890
progress 25% @chr4:88413077, elapsed 0.2s, est remaining 0.6s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 21138
progress 30% @chr5:147394035, elapsed 0.3s, est remaining 0.6s, peak mem 170MB, user 0.0s, sys 0.0s, output queue size 31171
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 170MB, user 0.0s, sys 0.0s, output queue size 41141
progress 40% @chr7:128801186, elapsed 0.3s, est remaining 0.5s, peak mem 170MB, user 0.0s, sys 0.0s, output queue size 50606
progress 45% @chr9:1056216, elapsed 0.4s, est remaining 0.5s, peak mem 284MB, user 0.0s, sys 0.0s, output queue size 7280
progress 50% @chr10:32292496, elapsed 0.4s, est remaining 0.4s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 17210
progress 55% @chr11:48216810, elapsed 0.5s, est remaining 0.4s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 27677
progress 60% @chr12:21912872, elapsed 0.5s, est remaining 0.3s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 37227
progress 65% @chr13:49255839, elapsed 0.6s, est remaining 0.3s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 48281
progress 70% @chr15:42684116, elapsed 0.6s, est remaining 0.3s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 58320
progress 75% @chr16:30902078, elapsed 0.7s, est remaining 0.2s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 67879
progress 80% @chr17:42543028, elapsed 0.7s, est remaining 0.2s, peak mem 299MB, user 0.0s, sys 0.1s, output queue size 78567
progress 85% @chr19:5622530, elapsed 0.8s, est remaining 0.1s, peak mem 326MB, user 0.0s, sys 0.1s, output queue size 88976
progress 90% @chr19:55651283, elapsed 0.8s, est remaining 0.1s, peak mem 326MB, user 0.0s, sys 0.1s, output queue size 98474
progress 95% @chr22:36933787, elapsed 1.2s, est remaining 0.1s, peak mem 2477MB, user 5.3s, sys 3.2s, output queue size 3228
progress 100% @chrY:57196336, elapsed 1.3s, est remaining 0.0s, peak mem 2477MB, user 5.5s, sys 3.2s, output queue size 5894
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: 51395354
reads: 1001089
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.641 user 0.141 sys 2.149 real
done: 1 calls 0.435 user 0.159 sys 0.593 real
execute: 1 calls 0.002 user 0.010 sys 1.263 real
fetch_reads: 208647 calls 0.127 user 0.002 sys 0.157 real
fetch_ref: 2042 calls 0.011 user 0.015 sys 0.040 real
fetch_vcf: 2042 calls 0.815 user 0.049 sys 0.912 real
idle: 92 calls 0.001 user 0.004 sys 31.803 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2207 calls 3.400 user 2.884 sys 7.043 real
overall: 2597912576 mem 9.265 user 22.193 sys 2.643 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