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/89/367c535ff2f0c527efeb80b165cce4/Sig_18_tissue.md.bam.bai 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/89/367c535ff2f0c527efeb80b165cce4/Sig_18_tissue.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/b242f48421014af2e2aef37cd7b2a5/.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/2c/b242f48421014af2e2aef37cd7b2a5/.command.run 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_tissue.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_tissue.table This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:119911554, elapsed 0.0s, est remaining 0.8s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 3881 progress 10% @chr2:19982463, elapsed 0.1s, est remaining 0.7s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 4041 progress 15% @chr2:189036616, elapsed 0.1s, est remaining 0.6s, peak mem 182MB, user 0.0s, sys 0.0s, output queue size 14437 progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.6s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 2973 progress 25% @chr4:88417425, elapsed 0.2s, est remaining 0.6s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 13242 progress 30% @chr5:146507873, elapsed 0.2s, est remaining 0.5s, peak mem 209MB, user 0.0s, sys 0.0s, output queue size 23280 progress 35% @chr6:125995967, elapsed 0.3s, est remaining 0.5s, peak mem 209MB, user 0.0s, sys 0.0s, output queue size 33226 progress 40% @chr7:128754529, elapsed 0.3s, est remaining 0.4s, peak mem 218MB, user 0.0s, sys 0.0s, output queue size 42716 progress 45% @chr9:2039466, elapsed 0.3s, est remaining 0.4s, peak mem 370MB, user 0.0s, sys 0.1s, output queue size 52086 progress 50% @chr10:32022020, elapsed 0.4s, est remaining 0.4s, peak mem 410MB, user 0.0s, sys 0.1s, output queue size 17211 progress 55% @chr11:48488793, elapsed 0.4s, est remaining 0.3s, peak mem 437MB, user 0.0s, sys 0.1s, output queue size 27673 progress 60% @chr12:22490123, elapsed 0.4s, est remaining 0.3s, peak mem 442MB, user 0.0s, sys 0.1s, output queue size 37254 progress 65% @chr13:49220338, elapsed 0.5s, est remaining 0.2s, peak mem 470MB, user 0.0s, sys 0.1s, output queue size 48273 progress 70% @chr15:42684116, elapsed 0.5s, est remaining 0.2s, peak mem 491MB, user 0.0s, sys 0.1s, output queue size 58304 progress 75% @chr16:30971378, elapsed 0.5s, est remaining 0.2s, peak mem 491MB, user 0.0s, sys 0.1s, output queue size 67887 progress 80% @chr17:42563961, elapsed 0.6s, est remaining 0.1s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 78567 progress 85% @chr19:5645337, elapsed 0.6s, est remaining 0.1s, peak mem 500MB, user 0.0s, sys 0.1s, output queue size 88969 progress 90% @chr19:55692951, elapsed 0.6s, est remaining 0.1s, peak mem 509MB, user 0.0s, sys 0.1s, output queue size 98474 progress 95% @chr22:36525664, elapsed 1.1s, est remaining 0.1s, peak mem 2498MB, user 7.9s, sys 2.2s, output queue size 108 progress 100% @chrY:57075987, elapsed 1.1s, est remaining 0.0s, peak mem 2498MB, user 7.9s, sys 2.2s, output queue size 1481 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.83 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: 50044781 reads: 1001838 contig: 201779 intervals 37922265 bases advance: 208647 calls 1.739 user 0.119 sys 2.160 real done: 1 calls 0.235 user 0.109 sys 0.353 real execute: 1 calls 0.000 user 0.010 sys 1.111 real fetch_reads: 208647 calls 0.119 user 0.001 sys 0.163 real fetch_ref: 2079 calls 0.008 user 0.009 sys 0.021 real fetch_vcf: 2079 calls 0.691 user 0.027 sys 0.976 real idle: 92 calls 0.003 user 0.001 sys 31.446 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 2294 calls 6.509 user 2.055 sys 8.970 real overall: 2620186624 mem 11.574 user 7.611 sys 2.472 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