File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/.command.log
Size
3.5 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER (659_bTo-N1-BDNA-1_B23KFG5LT4_1)
Attempt

Content

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  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/58ed24cfc74fe3aa25c98ba907ee11/659_bTo-N1-BDNA-1_B23KFG5LT4_1.entropy.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_locus_fp_rates.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_rf_model_v4.joblib
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_boosted_exons.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_blacklist.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/snv_fp_regions.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/27/51397b16e322fd631f3ffe5008ba81/659_bTo-N1-BDNA-1_B23KFG5LT4_1.entropy.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_rf_model_v7.joblib
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_low_depth.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_fp_regions.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7b/4c0d18e23be13f7dcb703b2a8d5b5e/.command.run
==> STAGING COMPLETE (19 inputs)

INFO: Loading models...
INFO: Reading VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.entropy.vcf.gz
WARNING: Some variants missing INFO fields: {'QD'}
INFO: Loaded 31092 variants (28988 SNVs, 2104 INDELs)
INFO:   INDEL entropy: 1932 present, 172 missing (using -1 sentinel)
INFO: Annotating with BED files...
INFO:   Blacklist hits: 1094
INFO:   Low depth hits: 212
INFO:   Boosted exon hits: 5970
INFO:   SNV FP region hits: 3679
INFO:   INDEL FP region hits: 1377
INFO:   INDEL FP rate lookups (TSV): 15241 variant keys loaded
INFO:   RepeatMasker hits: 1637
INFO: Applying models...
INFO: Results: 26764 PASS (25394 SNV, 1370 INDEL), 4328 RF_FAIL
INFO: Writing output VCF: 659_bTo-N1-BDNA-1_B23KFG5LT4_1.haplotyper_rf.rf_filtered.vcf.gz
INFO: Done!