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/89/a81db754cf0b002b753b29e841b8f1/1136_3LU-T1-TDNA-1_A23MHWWLT4_1.md.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/dd1f4ef651f78645bbfd207daf2b32/.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/41/dd1f4ef651f78645bbfd207daf2b32/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/a81db754cf0b002b753b29e841b8f1/1136_3LU-T1-TDNA-1_A23MHWWLT4_1.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 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.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 1136_3LU-T1-TDNA-1_A23MHWWLT4_1.table This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:119513834, elapsed 9.1s, est remaining 172.9s, peak mem 5647MB, user 240.8s, sys 5.6s, output queue size 179 progress 10% @chr2:17780621, elapsed 19.1s, est remaining 171.6s, peak mem 6824MB, user 509.6s, sys 8.5s, output queue size 1153 progress 15% @chr2:185799697, elapsed 30.6s, est remaining 173.4s, peak mem 8361MB, user 824.5s, sys 12.1s, output queue size 240 progress 20% @chr3:98819202, elapsed 40.1s, est remaining 160.4s, peak mem 8361MB, user 1080.8s, sys 13.9s, output queue size 440 progress 25% @chr4:88463855, elapsed 49.0s, est remaining 146.9s, peak mem 8361MB, user 1318.2s, sys 15.7s, output queue size 87 progress 30% @chr5:147400692, elapsed 55.8s, est remaining 130.3s, peak mem 8504MB, user 1497.9s, sys 17.2s, output queue size 208 progress 35% @chr6:132401163, elapsed 66.2s, est remaining 123.0s, peak mem 8693MB, user 1775.7s, sys 19.1s, output queue size 642 progress 40% @chr7:128903727, elapsed 78.8s, est remaining 118.2s, peak mem 9563MB, user 2109.9s, sys 21.6s, output queue size 1468 progress 45% @chr9:2039101, elapsed 93.4s, est remaining 114.2s, peak mem 15041MB, user 2517.8s, sys 27.7s, output queue size 18 progress 50% @chr10:33330708, elapsed 103.5s, est remaining 103.5s, peak mem 15041MB, user 2792.2s, sys 29.7s, output queue size 108 progress 55% @chr11:48164380, elapsed 112.3s, est remaining 91.9s, peak mem 15041MB, user 3026.5s, sys 31.2s, output queue size 15 progress 60% @chr12:25017134, elapsed 122.5s, est remaining 81.7s, peak mem 15041MB, user 3301.0s, sys 33.1s, output queue size 752 progress 65% @chr13:49702386, elapsed 131.9s, est remaining 71.0s, peak mem 15041MB, user 3554.9s, sys 34.9s, output queue size 569 progress 70% @chr15:43037773, elapsed 141.3s, est remaining 60.6s, peak mem 15041MB, user 3808.2s, sys 36.4s, output queue size 455 progress 75% @chr16:30953185, elapsed 153.9s, est remaining 51.3s, peak mem 15041MB, user 4157.7s, sys 39.1s, output queue size 32 progress 80% @chr17:42698618, elapsed 166.1s, est remaining 41.5s, peak mem 15041MB, user 4491.6s, sys 41.2s, output queue size 708 progress 85% @chr19:5693552, elapsed 175.6s, est remaining 31.0s, peak mem 15041MB, user 4752.2s, sys 42.8s, output queue size 404 progress 90% @chr19:55772602, elapsed 184.5s, est remaining 20.5s, peak mem 15041MB, user 4992.6s, sys 44.3s, output queue size 90 progress 95% @chr22:36864919, elapsed 197.1s, est remaining 10.4s, peak mem 15041MB, user 5340.2s, sys 46.6s, output queue size 856 progress 100% @chr6_GL000254v2_alt:3881705, elapsed 203.5s, est remaining 0.0s, peak mem 15041MB, user 5509.1s, sys 47.9s, output queue size 1 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: 77410294291 reads: 1436635500 contig: 201779 intervals 37922265 bases advance: 208647 calls 2966.799 user 39.608 sys 3097.735 real done: 1 calls 0.235 user 0.736 sys 0.979 real execute: 1 calls 0.004 user 0.011 sys 203.510 real fetch_reads: 208647 calls 237.255 user 0.706 sys 243.958 real fetch_ref: 207423 calls 1.116 user 1.031 sys 2.170 real fetch_vcf: 207423 calls 81.033 user 2.545 sys 85.816 real idle: 121 calls 0.180 user 0.000 sys 63.235 real init: 1 calls 0.000 user 0.000 sys 0.000 real update: 483158 calls 2699.092 user 2.585 sys 2752.239 real overall: 15772069888 mem 6165.823 user 49.797 sys 206.201 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