File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/ffc9a8321ca5726bda127f9cdf5ccb/.command.log
Size
3.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (LungN_FFPE_L01_RNA_01_B23LG7FLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/ffc9a8321ca5726bda127f9cdf5ccb/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/87bd423e04ae644a2eab618fd6674e/LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/66/0d3f1535378a73fd3fdc06f8bebd8d/LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/starfusion/ctat_genome_lib_build_dir/ref_annot.gtf
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/protein_domains_hg38_GRCh38_v2.4.0.gff3
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/ffc9a8321ca5726bda127f9cdf5ccb/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/11/e5a6c86f6a9d0e547eb406a0c580ca/LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (8 inputs)

Loading annotation
Read 3041209 records
Warning in parseGtfAttribute("exon_number", exons) :
  Failed to parse 'exon_number' attribute of 8 record(s).
Loading protein domains
Read 134356 records
Drawing fusion #1: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: LungN_FFPE_L01_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Done