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/60/56ea3c18ce6e5e65353fa4cf065e29/.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/60/56ea3c18ce6e5e65353fa4cf065e29/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/Sig_18_Blood.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/25dc077a00a8ba972f2936f02d2b56/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 0.0s, est remaining 0.8s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 3125 progress 10% @chr2:19966724, elapsed 0.1s, est remaining 0.7s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 2516 progress 15% @chr2:189003982, elapsed 0.1s, est remaining 0.6s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 12908 progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.6s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 23393 progress 25% @chr4:88437711, elapsed 0.2s, est remaining 0.6s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 33646 progress 30% @chr5:146589947, elapsed 0.2s, est remaining 0.5s, peak mem 162MB, user 0.0s, sys 0.0s, output queue size 43686 progress 35% @chr6:127119291, elapsed 0.3s, est remaining 0.5s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 9394 progress 40% @chr7:128806237, elapsed 0.3s, est remaining 0.4s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 18866 progress 45% @chr9:990041, elapsed 0.3s, est remaining 0.4s, peak mem 261MB, user 0.0s, sys 0.0s, output queue size 28237 progress 50% @chr10:32009016, elapsed 0.4s, est remaining 0.4s, peak mem 291MB, user 0.0s, sys 0.0s, output queue size 38190 progress 55% @chr11:48216810, elapsed 0.4s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 48640 progress 60% @chr12:21910826, elapsed 0.4s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 58187 progress 65% @chr13:49191209, elapsed 0.5s, est remaining 0.3s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 69240 progress 70% @chr15:42684116, elapsed 0.5s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 79318 progress 75% @chr16:30888860, elapsed 0.5s, est remaining 0.2s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 88838 progress 80% @chr17:42543028, elapsed 0.6s, est remaining 0.1s, peak mem 300MB, user 0.0s, sys 0.0s, output queue size 99531 progress 85% @chr19:5648989, elapsed 0.6s, est remaining 0.1s, peak mem 327MB, user 0.0s, sys 0.0s, output queue size 109940 progress 90% @chr19:55663606, elapsed 0.7s, est remaining 0.1s, peak mem 327MB, user 0.0s, sys 0.0s, output queue size 119437 progress 95% @chr22:37086283, elapsed 1.0s, est remaining 0.1s, peak mem 2505MB, user 5.6s, sys 1.9s, output queue size 3254 progress 100% @chrY:57075987, elapsed 1.0s, est remaining 0.0s, peak mem 2505MB, user 5.8s, sys 1.9s, output queue size 6116 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: 52290606 reads: 1001133 contig: 201779 intervals 37922265 bases advance: 208647 calls 1.668 user 0.086 sys 2.072 real done: 1 calls 0.404 user 0.206 sys 0.617 real execute: 1 calls 0.005 user 0.011 sys 1.050 real fetch_reads: 208647 calls 0.037 user 0.000 sys 0.152 real fetch_ref: 2072 calls 0.034 user 0.007 sys 0.027 real fetch_vcf: 2072 calls 0.650 user 0.040 sys 0.927 real idle: 90 calls 0.002 user 0.003 sys 31.803 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 2257 calls 4.153 user 1.731 sys 6.430 real overall: 2626752512 mem 9.382 user 19.681 sys 2.460 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