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/09/6c748c2a37f9c7a56b367940d31b62/.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-rnd-pltf-dev-nextflow-scratch-01/work/3a/5d1ab9c272915d7c2a564cb796e95c/Sig_18_Blood.dv_only_sites.vcf.gz.tbi 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/09/6c748c2a37f9c7a56b367940d31b62/.command.run Downloading: s3://natera-platform-sandbox/pipeline-inputs/test_sarek/end_to_end_regression/01_preprocess_regression_fastqs/regression_preprocess__60492e9--20260310-034416/alignments/recalibrated/Sig_18_Blood/Sig_18_Blood.recalibrated.bam.bai Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/5d1ab9c272915d7c2a564cb796e95c/Sig_18_Blood.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/Sig_18_Blood/Sig_18_Blood.recalibrated.bam ==> 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 Sig_18_Blood.recalibrated.bam --algo Haplotyper --given Sig_18_Blood.dv_only_sites.vcf.gz --emit_mode variant Sig_18_Blood.forcecall.unfiltered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr2:29715498, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 109 progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 236 progress 15% @chr3:142523851, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 461 progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 642 progress 25% @chr7:5995514, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 774 progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 822 progress 35% @chr9:21967753, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 954 progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 89 progress 45% @chr11:61437623, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 203 progress 50% @chr12:11752419, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 383 progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 395 progress 60% @chr12:11855326, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 411 progress 65% @chr12:132667502, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.0s, output queue size 480 progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 654 progress 75% @chr15:89316396, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 813 progress 80% @chr17:7682559, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1044 progress 85% @chr17:39532155, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1225 progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1328 progress 95% @chr19:50417823, elapsed 0.0s, est remaining 0.0s, peak mem 51MB, user 0.0s, sys 0.1s, output queue size 1508 progress 100% @chr21:34787802, elapsed 0.2s, est remaining 0.0s, peak mem 123MB, user 0.3s, 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: 208827488 output file size: 22302 reads: 2481283 contig: 2712 intervals 851273 bases active: 5761 calls 0.000 user 0.000 sys 0.002 real advance: 3049 calls 0.170 user 0.048 sys 0.235 real calc: 5761 calls 0.019 user 0.001 sys 0.044 real clip_region: 7 calls 0.000 user 0.000 sys 0.004 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.001 user 0.001 sys 0.162 real fetch: 5761 calls 0.037 user 0.002 sys 0.020 real fetch_ref: 5768 calls 0.004 user 0.000 sys 0.025 real fetch_region: 7 calls 0.000 user 0.000 sys 0.003 real idle: 25 calls 0.009 user 0.004 sys 13.077 real init: 1 calls 0.000 user 0.010 sys 0.002 real region: 5761 calls 0.000 user 0.000 sys 0.008 real tracker: 5761 calls 0.000 user 0.000 sys 0.006 real overall: 129110016 mem 0.412 user 0.402 sys 1.214 real ls: cannot access '*.g.vcf.gz': No such file or directory ls: cannot access '*.g.vcf.gz.tbi': No such file or directory