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-rnd-pltf-dev-nextflow-scratch-01/work/9b/bade8d20bab6f5e8ab070c3d74f2a7/.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/e8/c0a67c1d98a52e016e1ee4b829f9ba/HCC1395_BL.recalibrated.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e8/c0a67c1d98a52e016e1ee4b829f9ba/HCC1395_BL.recalibrated.bam.bai Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/altera_intervals/scatter/chr1_69091-70008.bed.gz Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/bade8d20bab6f5e8ab070c3d74f2a7/.command.run Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz ==> STAGING COMPLETE (9 inputs) cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -r Homo_sapiens_assembly38.fasta -t 12 --interval chr1_69091-70008.bed.gz -i HCC1395_BL.recalibrated.bam --algo Haplotyper -d dbsnp_146.hg38.vcf.gz --emit_mode variant germline_control_1.haplotyper.chr1_69091-70008.bed.unfiltered.vcf.gz This software is licensed to bgold@natera.com by Sentieon Inc. progress 5% @chr1:18365223, elapsed 0.1s, est remaining 1.6s, peak mem 93MB, user 0.1s, sys 0.3s, output queue size 1141 progress 10% @chr1:37752876, elapsed 0.2s, est remaining 1.5s, peak mem 103MB, user 0.2s, sys 0.7s, output queue size 3799 progress 15% @chr1:65408641, elapsed 0.3s, est remaining 1.5s, peak mem 116MB, user 0.3s, sys 1.2s, output queue size 6526 progress 20% @chr1:113825142, elapsed 0.4s, est remaining 1.4s, peak mem 127MB, user 0.4s, sys 1.7s, output queue size 9282 progress 25% @chr1:155238517, elapsed 0.4s, est remaining 1.3s, peak mem 136MB, user 0.5s, sys 2.2s, output queue size 11625 progress 30% @chr1:179118587, elapsed 0.5s, est remaining 1.2s, peak mem 147MB, user 0.6s, sys 2.6s, output queue size 14107 progress 35% @chr1:209795290, elapsed 0.6s, est remaining 1.1s, peak mem 156MB, user 0.7s, sys 3.0s, output queue size 16528 progress 40% @chr1:246907551, elapsed 0.7s, est remaining 1.0s, peak mem 165MB, user 0.8s, sys 3.2s, output queue size 18935 progress 45% @chr2:32549313, elapsed 0.8s, est remaining 0.9s, peak mem 175MB, user 0.9s, sys 3.6s, output queue size 2211 progress 50% @chr2:74461275, elapsed 0.9s, est remaining 0.9s, peak mem 184MB, user 1.0s, sys 4.0s, output queue size 4701 progress 55% @chr2:113499257, elapsed 0.9s, est remaining 0.8s, peak mem 193MB, user 1.1s, sys 4.5s, output queue size 7230 progress 60% @chr2:170993780, elapsed 1.0s, est remaining 0.7s, peak mem 204MB, user 1.2s, sys 5.0s, output queue size 9927 progress 65% @chr2:202695881, elapsed 1.1s, est remaining 0.6s, peak mem 214MB, user 1.3s, sys 5.4s, output queue size 12199 progress 70% @chr2:233772261, elapsed 1.2s, est remaining 0.5s, peak mem 223MB, user 1.4s, sys 5.8s, output queue size 14677 progress 75% @chr3:25626560, elapsed 1.3s, est remaining 0.4s, peak mem 232MB, user 1.5s, sys 6.3s, output queue size 16904 progress 80% @chr3:49804181, elapsed 1.4s, est remaining 0.3s, peak mem 241MB, user 1.6s, sys 6.8s, output queue size 19378 progress 85% @chr3:101859272, elapsed 1.5s, est remaining 0.3s, peak mem 254MB, user 1.7s, sys 7.3s, output queue size 22010 progress 90% @chr3:139561010, elapsed 1.6s, est remaining 0.2s, peak mem 264MB, user 1.8s, sys 7.8s, output queue size 24605 progress 95% @chr3:187741772, elapsed 1.7s, est remaining 0.1s, peak mem 273MB, user 1.9s, sys 8.1s, output queue size 27022 progress 100% @chr4:27017711, elapsed 1.7s, est remaining 0.0s, peak mem 281MB, user 2.0s, sys 8.5s, output queue size 29251 sw version: sentieon-genomics-202308.03 os version: Linux 6.12.83 cpu vendor: GenuineIntel signature: 00050657 features: 1f8bfbff fffa3203 extended: d19f47ab 00000018 amd bits: 2c100800 00000121 brand: Intel(R) Xeon(R) Platinum 8259CL CPU @ 2.50GHz threads: 12 max 64 algo: Haplotyper license: sentieon:Haplotyper=12 input file size: 71692772 output file size: 22306 reads: 1001089 contig: 49651 intervals 9000373 bases active: 100735 calls 0.021 user 0.002 sys 0.062 real advance: 51084 calls 0.047 user 0.070 sys 0.062 real calc: 100735 calls 0.029 user 0.013 sys 0.063 real done: 1 calls 0.000 user 0.000 sys 0.003 real execute: 1 calls 0.001 user 0.011 sys 3.211 real fetch: 100735 calls 0.010 user 0.012 sys 0.065 real fetch_ref: 100735 calls 0.334 user 0.080 sys 0.746 real idle: 51 calls 0.002 user 0.003 sys 30.571 real init: 1 calls 0.049 user 0.021 sys 0.067 real region: 100735 calls 0.016 user 0.023 sys 0.069 real tracker: 100735 calls 0.139 user 0.010 sys 0.230 real overall: 295243776 mem 2.888 user 11.906 sys 4.401 real ls: cannot access '*.g.vcf.gz': No such file or directory ls: cannot access '*.g.vcf.gz.tbi': No such file or directory