Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/0a286d0e2dbfa525b9d7b3eee89824/.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-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/f6c9539b5e75eea75fe4317d9da1b2/HCC1395_BL.dv_only_sites.vcf.gz Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/HCC1395_BL/HCC1395_BL.recalibrated.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/germline_rescue_targets.bed Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a2/0a286d0e2dbfa525b9d7b3eee89824/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/98/f6c9539b5e75eea75fe4317d9da1b2/HCC1395_BL.dv_only_sites.vcf.gz.tbi ==> STAGING COMPLETE (9 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval germline_rescue_targets.bed -i HCC1395_BL.recalibrated.bam --algo Haplotyper --given HCC1395_BL.dv_only_sites.vcf.gz --emit_mode variant HCC1395_BL.forcecall.unfiltered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr2:29531915, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 111 progress 10% @chr2:214794533, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 90 progress 15% @chr3:142523851, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 303 progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 484 progress 25% @chr7:5995514, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 616 progress 30% @chr7:55204953, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 658 progress 35% @chr9:21968576, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 795 progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 942 progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1056 progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1238 progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1251 progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1268 progress 65% @chr12:132660824, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1330 progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1509 progress 75% @chr15:89311648, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1666 progress 80% @chr17:7677279, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1897 progress 85% @chr17:39525864, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2079 progress 90% @chr17:61701914, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2178 progress 95% @chr19:52170836, elapsed 0.1s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 2362 progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 105MB, user 0.2s, sys 0.2s, output queue size 124 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: 12 max 384 algo: Haplotyper license: sentieon:Haplotyper=12 input file size: 163002590 output file size: 22292 reads: 1955548 contig: 2712 intervals 851273 bases active: 5761 calls 0.000 user 0.000 sys 0.002 real advance: 3049 calls 0.136 user 0.046 sys 0.199 real calc: 5761 calls 0.022 user 0.001 sys 0.030 real clip_region: 8 calls 0.000 user 0.004 sys 0.003 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.001 user 0.003 sys 0.145 real fetch: 5761 calls 0.009 user 0.002 sys 0.014 real fetch_ref: 5769 calls 0.001 user 0.000 sys 0.026 real fetch_region: 8 calls 0.000 user 0.000 sys 0.002 real idle: 26 calls 0.008 user 0.008 sys 12.801 real init: 1 calls 0.000 user 0.000 sys 0.002 real region: 5761 calls 0.000 user 0.004 sys 0.006 real tracker: 5761 calls 0.000 user 0.000 sys 0.007 real overall: 110231552 mem 0.341 user 0.526 sys 1.198 real ls: cannot access '*.g.vcf.gz': No such file or directory ls: cannot access '*.g.vcf.gz.tbi': No such file or directory