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/90/b9a654c2eb185e6f039bc9f9968f2d/HCC1395_tumor.md.bam.bai
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f5/c9deb0643295cf212b476c7f3fe9a7/.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/f5/c9deb0643295cf212b476c7f3fe9a7/.command.run
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/b9a654c2eb185e6f039bc9f9968f2d/HCC1395_tumor.md.bam
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_tumor.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_tumor.table
This software is licensed to bgold@natera.com by Sentieon Inc.
progress 5% @chr1:119921673, elapsed 0.1s, est remaining 1.0s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 4721
progress 10% @chr2:19980691, elapsed 0.1s, est remaining 0.9s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 2426
progress 15% @chr2:189052911, elapsed 0.1s, est remaining 0.8s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 12820
progress 20% @chr3:97961589, elapsed 0.2s, est remaining 0.8s, peak mem 161MB, user 0.0s, sys 0.0s, output queue size 23309
progress 25% @chr4:88457270, elapsed 0.2s, est remaining 0.7s, peak mem 164MB, user 0.0s, sys 0.0s, output queue size 33553
progress 30% @chr5:147408728, elapsed 0.3s, est remaining 0.6s, peak mem 170MB, user 0.0s, sys 0.0s, output queue size 43599
progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.6s, peak mem 170MB, user 0.0s, sys 0.0s, output queue size 53544
progress 40% @chr7:128806688, elapsed 0.4s, est remaining 0.5s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 8903
progress 45% @chr9:745173, elapsed 0.4s, est remaining 0.5s, peak mem 344MB, user 0.0s, sys 0.0s, output queue size 18277
progress 50% @chr10:32292496, elapsed 0.4s, est remaining 0.4s, peak mem 346MB, user 0.0s, sys 0.1s, output queue size 28204
progress 55% @chr11:48245104, elapsed 0.5s, est remaining 0.4s, peak mem 346MB, user 0.0s, sys 0.1s, output queue size 38674
progress 60% @chr12:21508383, elapsed 0.5s, est remaining 0.3s, peak mem 355MB, user 0.0s, sys 0.1s, output queue size 48220
progress 65% @chr13:49220338, elapsed 0.6s, est remaining 0.3s, peak mem 355MB, user 0.0s, sys 0.1s, output queue size 59274
progress 70% @chr15:42651016, elapsed 0.6s, est remaining 0.3s, peak mem 364MB, user 0.0s, sys 0.1s, output queue size 69308
progress 75% @chr16:30771833, elapsed 0.6s, est remaining 0.2s, peak mem 364MB, user 0.0s, sys 0.1s, output queue size 78870
progress 80% @chr17:42563961, elapsed 0.7s, est remaining 0.2s, peak mem 364MB, user 0.0s, sys 0.1s, output queue size 89564
progress 85% @chr19:5641740, elapsed 0.7s, est remaining 0.1s, peak mem 400MB, user 0.0s, sys 0.1s, output queue size 99969
progress 90% @chr19:55692686, elapsed 0.8s, est remaining 0.1s, peak mem 400MB, user 0.0s, sys 0.1s, output queue size 109478
progress 95% @chr22:36495967, elapsed 1.1s, est remaining 0.1s, peak mem 2509MB, user 5.9s, sys 2.3s, output queue size 1047
progress 100% @chr6_GL000251v2_alt:3935152, elapsed 1.2s, est remaining 0.0s, peak mem 2509MB, user 5.9s, sys 2.3s, output queue size 1502
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 192
algo: QualCal
license: sentieon:QualCal=31
input file size: 50813899
reads: 1001320
contig: 201779 intervals 37922265 bases
advance: 208647 calls 1.709 user 0.086 sys 2.100 real
done: 1 calls 0.287 user 0.109 sys 0.403 real
execute: 1 calls 0.006 user 0.001 sys 1.171 real
fetch_reads: 208647 calls 0.032 user 0.000 sys 0.139 real
fetch_ref: 2048 calls 0.032 user 0.009 sys 0.022 real
fetch_vcf: 2048 calls 0.764 user 0.041 sys 0.908 real
idle: 92 calls 0.003 user 0.001 sys 31.652 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2195 calls 4.028 user 2.128 sys 6.542 real
overall: 2631389184 mem 10.420 user 11.424 sys 2.575 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