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/fb/4595d57f2512c3edbf9d75d6f729ae/HCC1395_tumor.md.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e0/a07cd5c8ddec0b91182b22597ebc21/.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/e0/a07cd5c8ddec0b91182b22597ebc21/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/4595d57f2512c3edbf9d75d6f729ae/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% @chr1:119893964, elapsed 0.0s, est remaining 0.9s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 3945 progress 10% @chr2:20000441, elapsed 0.1s, est remaining 0.8s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 8076 progress 15% @chr2:189050569, elapsed 0.1s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 77 progress 20% @chr3:97871842, elapsed 0.2s, est remaining 0.7s, peak mem 163MB, user 0.0s, sys 0.0s, output queue size 2053 progress 25% @chr4:88423860, elapsed 0.2s, est remaining 0.6s, peak mem 166MB, user 0.0s, sys 0.0s, output queue size 5204 progress 30% @chr5:147383441, elapsed 0.3s, est remaining 0.6s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 1305 progress 35% @chr6:127144950, elapsed 0.3s, est remaining 0.5s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 11246 progress 40% @chr7:128729902, elapsed 0.3s, est remaining 0.5s, peak mem 172MB, user 0.0s, sys 0.0s, output queue size 4077 progress 45% @chr9:2060816, elapsed 0.4s, est remaining 0.4s, peak mem 328MB, user 0.0s, sys 0.1s, output queue size 13459 progress 50% @chr10:32009016, elapsed 0.4s, est remaining 0.4s, peak mem 343MB, user 0.0s, sys 0.1s, output queue size 23388 progress 55% @chr11:48306223, elapsed 0.5s, est remaining 0.4s, peak mem 343MB, user 0.0s, sys 0.1s, output queue size 8542 progress 60% @chr12:21910826, elapsed 0.5s, est remaining 0.3s, peak mem 349MB, user 0.0s, sys 0.1s, output queue size 973 progress 65% @chr13:49259346, elapsed 0.5s, est remaining 0.3s, peak mem 352MB, user 0.0s, sys 0.1s, output queue size 4785 progress 70% @chr15:42718752, elapsed 0.6s, est remaining 0.2s, peak mem 361MB, user 0.0s, sys 0.1s, output queue size 219 progress 75% @chr16:30946730, elapsed 0.6s, est remaining 0.2s, peak mem 361MB, user 0.0s, sys 0.1s, output queue size 758 progress 80% @chr17:42553794, elapsed 0.7s, est remaining 0.2s, peak mem 361MB, user 0.0s, sys 0.1s, output queue size 2502 progress 85% @chr19:5648016, elapsed 0.7s, est remaining 0.1s, peak mem 403MB, user 0.0s, sys 0.1s, output queue size 3836 progress 90% @chr19:55761801, elapsed 0.7s, est remaining 0.1s, peak mem 406MB, user 0.0s, sys 0.1s, output queue size 13326 progress 95% @chr22:36490008, elapsed 1.1s, est remaining 0.1s, peak mem 2485MB, user 6.5s, sys 2.0s, output queue size 994 progress 100% @chr6_GL000254v2_alt:3877871, elapsed 1.1s, est remaining 0.0s, peak mem 2485MB, user 6.5s, sys 2.0s, output queue size 3704 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.88 cpu vendor: GenuineIntel signature: 000a06d1 features: bfebfbff 7ffefbff extended: f3bfb7ef fb417ffe amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) 6975P-C threads: 31 max 384 algo: QualCal license: sentieon:QualCal=31 input file size: 50813906 reads: 1001320 contig: 201779 intervals 37922265 bases advance: 208647 calls 1.723 user 0.223 sys 2.306 real done: 1 calls 0.297 user 0.189 sys 0.494 real execute: 1 calls 0.007 user 0.001 sys 1.152 real fetch_reads: 208647 calls 0.076 user 0.006 sys 0.144 real fetch_ref: 2048 calls 0.049 user 0.007 sys 0.029 real fetch_vcf: 2048 calls 0.767 user 0.072 sys 0.992 real idle: 92 calls 0.002 user 0.002 sys 31.719 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 2195 calls 4.504 user 1.665 sys 7.273 real overall: 2605789184 mem 9.322 user 10.133 sys 2.543 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