File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/ad0fb7d42bd0bbab26371c2b05e256/.command.log
Size
1.4 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1)
Attempt

Content

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  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/b9/ad0fb7d42bd0bbab26371c2b05e256/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/d6297369b4aadbfede6f9510bd58c8/1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1.manta_fusion.somatic_sv.vcf.gz
  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/b9/ad0fb7d42bd0bbab26371c2b05e256/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/d6297369b4aadbfede6f9510bd58c8/1029_032-T1-TDNA-1_23K7YCLT4_1_vs_1029_032-N1-BDNA-1_235YY7LT3_1.manta_fusion.somatic_sv.vcf.gz.tbi
==> 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 (['1029_032-N1-BDNA-1_235YY7LT3_1', '1029_032-T1-TDNA-1_23K7YCLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.