File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/73b8d93dc6b1308f2b2ff5123a0a99/.command.log
Size
1.5 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_GERMLINE_ALL:BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER_RF:GT_CORRECTION (Sig_18_Blood)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/22/73b8d93dc6b1308f2b2ff5123a0a99/.command.sh
  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-rnd-pltf-dev-nextflow-scratch-01/work/22/73b8d93dc6b1308f2b2ff5123a0a99/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/1ea5eeaeb007f3ae587a28f47b4a6a/Sig_18_Blood.haplotyper_rf.rf_filtered.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fd/1ea5eeaeb007f3ae587a28f47b4a6a/Sig_18_Blood.haplotyper_rf.rf_filtered.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/RF_Models/rf_repeatmasker.bed.gz
==> STAGING COMPLETE (7 inputs)

INFO: Loading GT correction model: gt_correction_model_v2.joblib
INFO: GT correction threshold: 0.5
INFO: Reading VCF: Sig_18_Blood.haplotyper_rf.rf_filtered.vcf.gz
INFO: Total variants: 395, PASS INDELs to evaluate: 18
INFO: Annotating PASS INDELs with Simple_repeat...
INFO:   Simple_repeat hits: 0
INFO: Predicting genotypes...
INFO: Writing output VCF: Sig_18_Blood.haplotyper_rf.gt_corrected.vcf.gz
INFO: GT corrections applied:
INFO:   Het -> Hom: 0
INFO:   Hom -> Het: 0
INFO:   Unchanged:  18
INFO: Done!