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/74/3e208978cc459a8fec02c3c4fcb9f6/germline_control_1.dv_only_sites.vcf.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c3/74ed88cce728ddd6b954d5ee1fe874/.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/1a/a95586b1b08a697566ea24e2f6d852/HCC1395_BL.recalibrated.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1a/a95586b1b08a697566ea24e2f6d852/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/c3/74ed88cce728ddd6b954d5ee1fe874/.command.run Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/74/3e208978cc459a8fec02c3c4fcb9f6/germline_control_1.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 germline_control_1.dv_only_sites.vcf.gz --emit_mode variant germline_control_1.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 49MB, user 0.0s, sys 0.0s, output queue size 16 progress 10% @chr2:214725647, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 43 progress 15% @chr3:142540904, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 263 progress 20% @chr5:112818952, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 445 progress 25% @chr7:5999106, elapsed 0.0s, est remaining 0.1s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 579 progress 30% @chr7:55176897, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 622 progress 35% @chr9:21970761, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 756 progress 40% @chr10:43111197, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 903 progress 45% @chr11:64803513, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.0s, sys 0.0s, output queue size 1018 progress 50% @chr12:11770919, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 1200 progress 55% @chr12:11796959, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 145 progress 60% @chr12:11831519, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 163 progress 65% @chr12:132663994, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 221 progress 70% @chr14:65075125, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 403 progress 75% @chr15:89305104, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.0s, output queue size 553 progress 80% @chr17:7679679, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.1s, output queue size 787 progress 85% @chr17:39530604, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.1s, output queue size 969 progress 90% @chr17:61679140, elapsed 0.0s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.1s, output queue size 1071 progress 95% @chr19:52170836, elapsed 0.1s, est remaining 0.0s, peak mem 49MB, user 0.1s, sys 0.1s, output queue size 1255 progress 100% @chr21:34787802, elapsed 0.1s, est remaining 0.0s, peak mem 84MB, user 0.1s, sys 0.1s, output queue size 124 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: 12 max 192 algo: Haplotyper license: sentieon:Haplotyper=12 input file size: 71692772 output file size: 22310 reads: 1001089 contig: 2712 intervals 851273 bases active: 5761 calls 0.000 user 0.000 sys 0.002 real advance: 3049 calls 0.046 user 0.026 sys 0.105 real calc: 5761 calls 0.005 user 0.000 sys 0.018 real clip_region: 7 calls 0.000 user 0.000 sys 0.002 real done: 1 calls 0.000 user 0.000 sys 0.002 real execute: 1 calls 0.003 user 0.005 sys 0.100 real fetch: 5761 calls 0.003 user 0.010 sys 0.009 real fetch_ref: 5768 calls 0.006 user 0.000 sys 0.025 real fetch_region: 7 calls 0.000 user 0.002 sys 0.001 real idle: 25 calls 0.006 user 0.019 sys 12.427 real init: 1 calls 0.000 user 0.000 sys 0.002 real region: 5761 calls 0.000 user 0.002 sys 0.004 real tracker: 5761 calls 0.000 user 0.000 sys 0.007 real overall: 88346624 mem 0.226 user 0.377 sys 1.153 real ls: cannot access '*.g.vcf.gz': No such file or directory ls: cannot access '*.g.vcf.gz.tbi': No such file or directory