File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/af3be6d7f004d9689aeca091057032/.command.log
Size
1.3 KB
Task
NFCORE_SAREK:SAREK:BAM_CHIP_DETECTION:SCORE_CHIP_VARIANTS (1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fa/af3be6d7f004d9689aeca091057032/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b5075d0c6998bf9e4fbd2a0c90cc7b/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.readcount_annotated.vcf.gz
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/gene_tiers.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/b5075d0c6998bf9e4fbd2a0c90cc7b/1029_BTOJ-N1-BDNA-1_B23KGCJLT4_1.readcount_annotated.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/CHIP/cosmic_heme.tsv.gz
  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/fa/af3be6d7f004d9689aeca091057032/.command.run
==> STAGING COMPLETE (7 inputs)

[INFO] Scoring params: TLOD>=60, blood:tumor>=2.0
[INFO] Blacklist: 68611 positions
[INFO] COSMIC heme: 113942 variants
[INFO] Gene tiers: 19423 genes
[INFO] Pass 1: Reading and scoring variants...
[INFO] Read 32270 variants
[INFO] Pass 2: Writing scored variants...
[INFO] Scored: 2 CHIP_PASS, 32268 CHIP_FAIL, 32270 total