File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/f7b350021f5be78745e459d1409dc9/.command.log
Size
1.6 KB
Task
NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:PRE_FILTER_CHIP_CANDIDATES (HCC1395_BL)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/d63291d60063ef473ef017dd4ed2d7/HCC1395_BL.CHIP_PON.merged.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/f7b350021f5be78745e459d1409dc9/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cohort_blacklist.bed.gz
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/19/f7b350021f5be78745e459d1409dc9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4f/d63291d60063ef473ef017dd4ed2d7/HCC1395_BL.CHIP_PON.merged.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_family_blacklist.bed.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/encode_blacklist.bed.gz
==> STAGING COMPLETE (8 inputs)

[INFO] Loading resources...
[INFO] Cohort blacklist: 68611 positions
[INFO] Gene-family blacklist: 76473 positions
[INFO] ENCODE blacklist: 636 intervals
[INFO] Gene tiers: 19423 genes, max_tier=2
[INFO] Pre-filter: 0 PASS, 291 FAIL, 291 total
[INFO] Survivors BED: 0 sites written to HCC1395_BL.survivors.bed
[INFO]   no_functional_impact: 212
[INFO]   hard_filter_reject: 50
[INFO]   cohort_blacklist: 18
[INFO]   gene_not_in_universe: 9
[INFO]   pon_artifact: 1
[INFO]   gene_family_blacklist: 1