File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8c19fc2bf5d00961badc32b6e45d2d/.command.log
Size
1.3 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (pos_somatic_038)
Attempt

Content

View in new tab 
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/9fcd0c97a8105ad827bb45405056ac/pos_somatic_038.manta_fusion.somatic_sv.vcf.gz.tbi
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/foresight_panel_for_manta.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8c19fc2bf5d00961badc32b6e45d2d/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/MantaFusion/protein_coding_genes.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3d/8c19fc2bf5d00961badc32b6e45d2d/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/42/9fcd0c97a8105ad827bb45405056ac/pos_somatic_038.manta_fusion.somatic_sv.vcf.gz
==> STAGING COMPLETE (6 inputs)

[annotateFusionVcf] Loading gene BED: protein_coding_genes.bed
[annotateFusionVcf] Loading actionable BED: foresight_panel_for_manta.bed
[annotateFusionVcf] Annotating VCF...
[annotateFusionVcf] WARNING: could not identify tumor sample by name (['NA12878_c_0002_gDNA_0005_B23KYWJLT4_1', 'FFPE_HD789_01_p2_gDNA_03_A23GW7HLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.