File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/7f/34bb4d0efbfc7afb2ecf190f750b06/.command.log
Size
1.4 KB
Task
NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_MANTA_FUSION:MANTA_FUSION_ANNOTATE (1173_CRL-T1-TDNA-SLD-01_A23T7FVLT4_1_vs_1173_CRL-N1-BDNA-01_A23MHW3LT4_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/7f/34bb4d0efbfc7afb2ecf190f750b06/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/934ff002c69fb4b6ea702fe6e3222e/1173_CRL-T1-TDNA-SLD-01_A23T7FVLT4_1_vs_1173_CRL-N1-BDNA-01_A23MHW3LT4_1.manta_fusion.somatic_sv.vcf.gz.tbi
  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/7f/34bb4d0efbfc7afb2ecf190f750b06/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/83/934ff002c69fb4b6ea702fe6e3222e/1173_CRL-T1-TDNA-SLD-01_A23T7FVLT4_1_vs_1173_CRL-N1-BDNA-01_A23MHW3LT4_1.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 (['1173_CRL-N1-BDNA-01_A23MHW3LT4_1', '1173_CRL-T1-TDNA-SLD-01_A23T7FVLT4_1']) — falling back to positional heuristic (column 1). FUSION_TUMOR_VAF / FUSION_NORMAL_VAF may be incorrect.
[annotateFusionVcf] Done.