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/64/549a0e17c41114d7459188935c7bf0/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/17/e6d972a8759391738a74fe64d7ff55/.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/64/549a0e17c41114d7459188935c7bf0/HCC1395_BL.md.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/e6d972a8759391738a74fe64d7ff55/.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 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% @chr1:119802828, elapsed 0.0s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 1657 progress 10% @chr2:19993111, elapsed 0.1s, est remaining 0.6s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 11688 progress 15% @chr2:189054159, elapsed 0.1s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 3500 progress 20% @chr3:97871842, elapsed 0.1s, est remaining 0.6s, peak mem 165MB, user 0.0s, sys 0.0s, output queue size 13965 progress 25% @chr4:88405554, elapsed 0.2s, est remaining 0.5s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 24232 progress 30% @chr5:147415709, elapsed 0.2s, est remaining 0.5s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 34282 progress 35% @chr6:127137390, elapsed 0.2s, est remaining 0.5s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 44218 progress 40% @chr7:128801186, elapsed 0.3s, est remaining 0.4s, peak mem 174MB, user 0.0s, sys 0.0s, output queue size 53706 progress 45% @chr9:2007196, elapsed 0.3s, est remaining 0.4s, peak mem 292MB, user 0.0s, sys 0.0s, output queue size 63080 progress 50% @chr10:32293592, elapsed 0.3s, est remaining 0.3s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 901 progress 55% @chr11:48139486, elapsed 0.4s, est remaining 0.3s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 11368 progress 60% @chr12:21894032, elapsed 0.4s, est remaining 0.3s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 20915 progress 65% @chr13:49278350, elapsed 0.4s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 31969 progress 70% @chr15:42566607, elapsed 0.5s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 42002 progress 75% @chr16:30892840, elapsed 0.5s, est remaining 0.2s, peak mem 307MB, user 0.0s, sys 0.0s, output queue size 51568 progress 80% @chr17:42466429, elapsed 0.5s, est remaining 0.1s, peak mem 307MB, user 0.0s, sys 0.1s, output queue size 62261 progress 85% @chr19:5661518, elapsed 0.6s, est remaining 0.1s, peak mem 334MB, user 0.0s, sys 0.1s, output queue size 72666 progress 90% @chr19:55642509, elapsed 0.6s, est remaining 0.1s, peak mem 334MB, user 0.0s, sys 0.1s, output queue size 82170 progress 95% @chr22:36923717, elapsed 0.9s, est remaining 0.0s, peak mem 2539MB, user 6.2s, sys 1.7s, output queue size 2843 progress 100% @chrY:25043946, elapsed 1.0s, est remaining 0.0s, peak mem 2539MB, user 6.3s, sys 1.7s, output queue size 9583 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: 51395361 reads: 1001089 contig: 201779 intervals 37922265 bases advance: 208647 calls 1.844 user 0.084 sys 2.122 real done: 1 calls 0.276 user 0.068 sys 0.345 real execute: 1 calls 0.003 user 0.011 sys 0.977 real fetch_reads: 208647 calls 0.067 user 0.000 sys 0.143 real fetch_ref: 2042 calls 0.005 user 0.012 sys 0.028 real fetch_vcf: 2042 calls 0.912 user 0.016 sys 0.951 real idle: 92 calls 0.003 user 0.001 sys 31.528 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 2207 calls 4.052 user 1.520 sys 6.238 real overall: 2663051264 mem 9.647 user 13.308 sys 2.340 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