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/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/Sig_18_tissue.md.bam.bai
  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/f5/a9e2ccd0c8e1b97d551b9ee4f0aee5/Sig_18_tissue.md.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c6/80a9dc8a13e20f7c49d544b48d618f/.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/c6/80a9dc8a13e20f7c49d544b48d618f/.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 (13 inputs)

cmdline: /opt/conda/share/sentieon-202308.03-3/libexec/driver -t 31 -r Homo_sapiens_assembly38.fasta -i Sig_18_tissue.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 Sig_18_tissue.table
This software is licensed to bgold@natera.com by Sentieon Inc.
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
No more license available for sentieon:QualCal
progress 5% @chr1:119911554, elapsed 600.1s, est remaining 11402.0s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 7504
progress 10% @chr2:19897869, elapsed 600.1s, est remaining 5401.2s, peak mem 173MB, user 0.0s, sys 0.0s, output queue size 9035
progress 15% @chr2:189060730, elapsed 600.2s, est remaining 3401.0s, peak mem 182MB, user 0.0s, sys 0.0s, output queue size 19430
progress 20% @chr3:97871842, elapsed 600.2s, est remaining 2400.8s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 29889
progress 25% @chr4:88396015, elapsed 600.2s, est remaining 1800.7s, peak mem 191MB, user 0.0s, sys 0.0s, output queue size 40158
progress 30% @chr5:146507873, elapsed 600.3s, est remaining 1400.7s, peak mem 212MB, user 0.0s, sys 0.0s, output queue size 3992
progress 35% @chr6:127144950, elapsed 600.3s, est remaining 1114.9s, peak mem 212MB, user 0.0s, sys 0.0s, output queue size 13933
progress 40% @chr7:128810139, elapsed 600.3s, est remaining 900.5s, peak mem 221MB, user 0.0s, sys 0.0s, output queue size 23428
progress 45% @chr9:990041, elapsed 600.4s, est remaining 733.8s, peak mem 328MB, user 0.0s, sys 0.0s, output queue size 32800
progress 50% @chr10:32634254, elapsed 600.4s, est remaining 600.4s, peak mem 410MB, user 0.0s, sys 0.1s, output queue size 42742
progress 55% @chr11:48263861, elapsed 600.4s, est remaining 491.3s, peak mem 446MB, user 0.0s, sys 0.1s, output queue size 53194
progress 60% @chr12:22471399, elapsed 600.5s, est remaining 400.3s, peak mem 452MB, user 0.0s, sys 0.1s, output queue size 62786
progress 65% @chr13:49136332, elapsed 600.5s, est remaining 323.4s, peak mem 479MB, user 0.0s, sys 0.1s, output queue size 73800
progress 70% @chr15:42684116, elapsed 600.6s, est remaining 257.4s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 83848
progress 75% @chr16:30947052, elapsed 600.6s, est remaining 200.2s, peak mem 502MB, user 0.0s, sys 0.1s, output queue size 93401
progress 80% @chr17:42562612, elapsed 600.7s, est remaining 150.2s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 104091
progress 85% @chr19:5653115, elapsed 600.7s, est remaining 106.0s, peak mem 511MB, user 0.0s, sys 0.1s, output queue size 114499
progress 90% @chr19:55712420, elapsed 600.8s, est remaining 66.8s, peak mem 520MB, user 0.0s, sys 0.1s, output queue size 123998
progress 95% @chr22:37011027, elapsed 601.3s, est remaining 31.6s, peak mem 2518MB, user 10.1s, sys 2.4s, output queue size 3258
progress 100% @chr6_GL000254v2_alt:3891538, elapsed 601.3s, est remaining 0.0s, peak mem 2518MB, user 10.4s, sys 2.4s, output queue size 4846
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: 50047064
reads: 1001838
contig: 201779 intervals 37922265 bases
advance: 208647 calls 2.186 user 0.101 sys 2.663 real
done: 1 calls 0.318 user 0.130 sys 0.452 real
execute: 1 calls 0.001 user 0.011 sys 601.347 real
fetch_reads: 208647 calls 0.148 user 0.009 sys 0.245 real
fetch_ref: 2079 calls 0.002 user 0.003 sys 0.024 real
fetch_vcf: 2079 calls 1.119 user 0.037 sys 1.208 real
idle: 60 calls 0.001 user 0.002 sys 31.011 real
init: 1 calls 0.000 user 0.000 sys 0.000 real
update: 2294 calls 8.669 user 2.244 sys 11.822 real
overall: 2640338944 mem 15.137 user 6.541 sys 602.751 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