Skip to content

Instantly share code, notes, and snippets.

@srynobio
Last active January 30, 2019 21:48
Show Gist options
  • Save srynobio/0f32eac8b337842dc0eada8803f441c3 to your computer and use it in GitHub Desktop.
Save srynobio/0f32eac8b337842dc0eada8803f441c3 to your computer and use it in GitHub Desktop.
cmdline: /sentieon-genomics-201808.03/libexec/driver --thread_count 30 -r /scratch/ucgd/lustre/common/data/Reference/GRCh38/human_g1k_v38_decoy_phix.fasta --interval /scratch/ucgd/lustre/common/data/Regions/GRCh38/UCGD.CDS.Region.bed --algo VarCal --vcf 17-10-27_Test-Yandell-Disease_merged.vcf.gz --var_type SNP --tranches_file 17-10-27_Test-Yandell-Disease_recal.tranches.snp --resource /scratch/ucgd/lustre/common/data/GATK_Bundle/GRCh38/hapmap_3.3.hg38.vcf.gz --resource_param hapmap,known=false,training=true,truth=true,prior=15.0 --resource /scratch/ucgd/lustre/common/data/GATK_Bundle/GRCh38/1000G_omni2.5.hg38.vcf.gz --resource_param omni,known=false,training=true,truth=true,prior=12.0 --resource /scratch/ucgd/lustre/common/data/GATK_Bundle/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz --resource_param 1000G,known=false,training=true,truth=false,prior=10.0 --resource /scratch/ucgd/lustre/common/data/GATK_Bundle/GRCh38/dbsnp_138.hg38.vcf.gz --resource_param dbsnp,known=true,training=false,truth=false,prior=2.0 17-10-27_Test-Yandell-Disease_recal.snp.vcf.gz --annotation AC --annotation AF --annotation AN --annotation BaseQRankSum --annotation DP --annotation ExcessHet --annotation FS --annotation InbreedingCoeff --annotation MLEAC --annotation MLEAF --annotation MQ --annotation MQRankSum --annotation QD --annotation RAW_MQ --annotation ReadPosRankSum --annotation SOR --annotation SAC --annotation AS_BaseQRankSum --annotation AS_FS --annotation AS_InbreedingCoeff --annotation AS_MQRankSum --annotation AS_QD --annotation AS_MQ --annotation AS_ReadPosRankSum --annotation AS_SOR
This software is licensed to ... by Sentieon Inc.
maxGaussians = 8
progress 5% @chr1:89712710, elapsed 0.3s, est remaining 5.4s, peak mem 184MB, user 7.8s, sys 0.2s, output queue size 2167
progress 10% @chr2:27058401, elapsed 0.5s, est remaining 4.9s, peak mem 192MB, user 15.3s, sys 0.4s, output queue size 1761
progress 15% @chr2:171976158, elapsed 0.8s, est remaining 4.8s, peak mem 197MB, user 23.7s, sys 0.6s, output queue size 2418
progress 20% @chr3:100283608, elapsed 1.1s, est remaining 4.5s, peak mem 208MB, user 31.4s, sys 0.7s, output queue size 5083
progress 25% @chr4:3500693, elapsed 1.4s, est remaining 4.3s, peak mem 208MB, user 40.6s, sys 0.9s, output queue size 3058
progress 30% @chr5:148120010, elapsed 1.8s, est remaining 4.1s, peak mem 209MB, user 50.1s, sys 1.2s, output queue size 1541
progress 35% @chr6:73818389, elapsed 2.1s, est remaining 3.8s, peak mem 211MB, user 57.9s, sys 1.3s, output queue size 4949
progress 40% @chr7:123959485, elapsed 2.4s, est remaining 3.6s, peak mem 232MB, user 67.3s, sys 1.5s, output queue size 1895
progress 45% @chr9:16966, elapsed 2.7s, est remaining 3.3s, peak mem 232MB, user 76.7s, sys 1.7s, output queue size 3479
progress 50% @chr10:75037837, elapsed 3.0s, est remaining 3.0s, peak mem 232MB, user 85.6s, sys 1.9s, output queue size 2337
progress 55% @chr11:56275640, elapsed 3.3s, est remaining 2.7s, peak mem 233MB, user 93.3s, sys 2.1s, output queue size 4473
progress 60% @chr12:53068156, elapsed 3.6s, est remaining 2.4s, peak mem 236MB, user 100.6s, sys 2.3s, output queue size 2459
progress 65% @chr13:48515206, elapsed 3.9s, est remaining 2.1s, peak mem 237MB, user 108.9s, sys 2.5s, output queue size 3051
progress 70% @chr15:51450130, elapsed 4.1s, est remaining 1.8s, peak mem 240MB, user 116.5s, sys 2.7s, output queue size 3755
progress 75% @chr16:89637633, elapsed 4.4s, est remaining 1.5s, peak mem 279MB, user 123.6s, sys 2.9s, output queue size 4988
progress 80% @chr17:57885230, elapsed 4.6s, est remaining 1.2s, peak mem 279MB, user 130.0s, sys 3.0s, output queue size 6130
progress 85% @chr19:3205940, elapsed 4.9s, est remaining 0.9s, peak mem 279MB, user 137.6s, sys 3.2s, output queue size 2034
progress 90% @chr19:45165128, elapsed 5.1s, est remaining 0.6s, peak mem 279MB, user 143.5s, sys 3.3s, output queue size 5959
progress 95% @chrX:3320009, elapsed 5.4s, est remaining 0.3s, peak mem 279MB, user 151.3s, sys 3.5s, output queue size 2867
progress 100% @chrX:148953581, elapsed 7.7s, est remaining 0.0s, peak mem 279MB, user 156.6s, sys 3.6s, output queue size 1429
data size = 175996
There is no training data for annotation RAW_MQ for var_type SNP. Please remove RAW_MQ from annotations
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment