.command.log - Workdir - NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (COLO829_tumor_100pct_rep1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d1/511f0729023e6a849021398c930ed2/.command.log
Size: 1.3 KB
Task: NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (COLO829_tumor_100pct_rep1)
Attempt

Content

  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/d1/511f0729023e6a849021398c930ed2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/ce35f6fb6fc537384616bfd91c3973/COLO829_tumor_100pct_rep1.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/d1/511f0729023e6a849021398c930ed2/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/ce35f6fb6fc537384616bfd91c3973/COLO829_tumor_100pct_rep1.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 (['COLO829BL_c_01_gDNA_0001_A237FLHLT3_1', 'COLO829_c_0001_gDNA_0001_B23H2NLLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.