File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/3dbfbb6694f447139e0e1bc6aa3ff6/.command.log
Size
1.4 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (659_bUW-T1-TDNA-1_B23KFCWLT4_1_vs_659_bUW-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/43/ca4fbbe5ffa7c7defa5fa602c57149/659_bUW-T1-TDNA-1_B23KFCWLT4_1_vs_659_bUW-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.vcf.gz
  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/43/ca4fbbe5ffa7c7defa5fa602c57149/659_bUW-T1-TDNA-1_B23KFCWLT4_1_vs_659_bUW-N1-BDNA-1_B23KGCJLT4_1.manta_fusion.somatic_sv.vcf.gz.tbi
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/88/3dbfbb6694f447139e0e1bc6aa3ff6/.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/88/3dbfbb6694f447139e0e1bc6aa3ff6/.command.run
==> 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 (['659_bUW-N1-BDNA-1_B23KGCJLT4_1', '659_bUW-T1-TDNA-1_B23KFCWLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.