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/f7/7df0dd603900a4e96831ac49153a79/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/f7/7df0dd603900a4e96831ac49153a79/Sig_18_tissue.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/12/86d61a71cffe6f28b3e8272858b33a/.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/12/86d61a71cffe6f28b3e8272858b33a/.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 5166 progress 10% @chr2:19989992, elapsed 0.1s, est remaining 0.7s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 7659 progress 15% @chr2:184935783, elapsed 0.1s, est remaining 0.7s, peak mem 182MB, user 0.0s, sys 0.0s, output queue size 3207 progress 20% @chr3:97949844, elapsed 0.2s, est remaining 0.6s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 13689 progress 25% @chr4:88383221, elapsed 0.2s, est remaining 0.6s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 23934 progress 30% @chr5:146463551, elapsed 0.2s, est remaining 0.5s, peak mem 210MB, user 0.0s, sys 0.0s, output queue size 9756 progress 35% @chr6:127144950, elapsed 0.3s, est remaining 0.5s, peak mem 210MB, user 0.0s, sys 0.0s, output queue size 19695 progress 40% @chr7:128806688, elapsed 0.3s, est remaining 0.4s, peak mem 219MB, user 0.0s, sys 0.0s, output queue size 29191 progress 45% @chr9:2047229, elapsed 0.3s, est remaining 0.4s, peak mem 347MB, user 0.0s, sys 0.0s, output queue size 38564 progress 50% @chr10:32567670, elapsed 0.4s, est remaining 0.4s, peak mem 402MB, user 0.0s, sys 0.1s, output queue size 6472 progress 55% @chr11:48324941, elapsed 0.4s, est remaining 0.3s, peak mem 438MB, user 0.0s, sys 0.1s, output queue size 16937 progress 60% @chr12:22493223, elapsed 0.4s, est remaining 0.3s, peak mem 441MB, user 0.0s, sys 0.1s, output queue size 26519 progress 65% @chr13:49267490, elapsed 0.4s, est remaining 0.2s, peak mem 465MB, user 0.0s, sys 0.1s, output queue size 37542 progress 70% @chr15:42724491, elapsed 0.5s, est remaining 0.2s, peak mem 492MB, user 0.0s, sys 0.1s, output queue size 47573 progress 75% @chr16:30781718, elapsed 0.5s, est remaining 0.2s, peak mem 492MB, user 0.0s, sys 0.1s, output queue size 57137 progress 80% @chr17:42562612, elapsed 0.5s, est remaining 0.1s, peak mem 503MB, user 0.0s, sys 0.1s, output queue size 67829 progress 85% @chr19:5687753, elapsed 0.6s, est remaining 0.1s, peak mem 503MB, user 0.0s, sys 0.1s, output queue size 78240 progress 90% @chr19:55731999, elapsed 0.6s, est remaining 0.1s, peak mem 513MB, user 0.0s, sys 0.1s, output queue size 87733 progress 95% @chr22:37136228, elapsed 1.0s, est remaining 0.1s, peak mem 2535MB, user 7.8s, sys 1.8s, output queue size 3260 progress 100% @chrY:14733452, elapsed 1.1s, est remaining 0.0s, peak mem 2535MB, user 8.0s, sys 1.8s, output queue size 1798 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000c06f2 features: bfebfbff 7ffefbff extended: f3bfb7ef fb417ffe amd bits: 2c100800 00000121 brand: INTEL(R) XEON(R) PLATINUM 8559C threads: 31 max 192 algo: QualCal license: sentieon:QualCal=31 input file size: 50047062 reads: 1001838 contig: 201779 intervals 37922265 bases advance: 208647 calls 1.864 user 0.115 sys 2.253 real done: 1 calls 0.313 user 0.078 sys 0.393 real execute: 1 calls 0.005 user 0.002 sys 1.058 real fetch_reads: 208647 calls 0.098 user 0.003 sys 0.154 real fetch_ref: 2079 calls 0.002 user 0.003 sys 0.025 real fetch_vcf: 2079 calls 0.864 user 0.106 sys 1.027 real idle: 92 calls 0.003 user 0.001 sys 31.698 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 2294 calls 6.432 user 1.533 sys 8.751 real overall: 2658881536 mem 11.736 user 3.629 sys 2.445 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