File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c8/32c0696c226bb7fa5929b0bb251944/.command.log
Size
3.4 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:SENTIEON_HAPLOTYPER_RF_FILTER (germline_control_2)
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-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/indel_locus_fp_rates.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3c/37272197d685e05b879fd06664db6c/germline_control_2.entropy.vcf.gz
  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/c8/32c0696c226bb7fa5929b0bb251944/.command.sh
  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-rnd-pltf-dev-nextflow-scratch-01/work/c6/b8e1db501e507ea01d5a51dc912ab2/germline_control_2.entropy.vcf.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/c8/32c0696c226bb7fa5929b0bb251944/.command.run
==> STAGING COMPLETE (19 inputs)

INFO: Loading models...
INFO: Reading VCF: germline_control_2.entropy.vcf.gz
INFO: Loaded 394 variants (369 SNVs, 25 INDELs)
INFO:   INDEL entropy: 23 present, 2 missing (using -1 sentinel)
INFO: Annotating with BED files...
INFO:   Blacklist hits: 8
INFO:   Low depth hits: 0
INFO:   Boosted exon hits: 90
INFO:   SNV FP region hits: 30
INFO:   INDEL FP region hits: 9
INFO:   INDEL FP rate lookups (TSV): 15241 variant keys loaded
INFO:   RepeatMasker hits: 30
INFO: Applying models...
INFO: Results: 354 PASS (336 SNV, 18 INDEL), 40 RF_FAIL
INFO: Writing output VCF: germline_control_2.haplotyper_rf.rf_filtered.vcf.gz
INFO: Done!