File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/3afaecde1dc89d015b413a62acdb6c/.command.log
Size
1.5 KB
Task
DAQ:CONTROL_VARIANT_CALLING:CONTROL_GERMLINE_VC:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION (germline_control_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/256f044c81edc6ea6c8bc3d2b1d652/germline_control_2.haplotyper_rf.rf_filtered.vcf.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/3afaecde1dc89d015b413a62acdb6c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/256f044c81edc6ea6c8bc3d2b1d652/germline_control_2.haplotyper_rf.rf_filtered.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/gt_correction_model_v2.joblib
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/48/3afaecde1dc89d015b413a62acdb6c/.command.run
==> STAGING COMPLETE (7 inputs)

INFO: Loading GT correction model: gt_correction_model_v2.joblib
INFO: GT correction threshold: 0.5
INFO: Reading VCF: germline_control_2.haplotyper_rf.rf_filtered.vcf.gz
INFO: Total variants: 394, PASS INDELs to evaluate: 18
INFO: Annotating PASS INDELs with Simple_repeat...
INFO:   Simple_repeat hits: 0
INFO: Predicting genotypes...
INFO: Writing output VCF: germline_control_2.haplotyper_rf.gt_corrected.vcf.gz
INFO: GT corrections applied:
INFO:   Het -> Hom: 0
INFO:   Hom -> Het: 0
INFO:   Unchanged:  18
INFO: Done!