File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7be12205e4476539ddf61e1eb69b3c/.command.log
Size
3.6 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/eebdeaa7e2bf48b2679dfae16d5c8c/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/7be12205e4476539ddf61e1eb69b3c/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f3/e928397933318d30a4344e8c6f0121/HeadNeckN_FFPE_L08_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-rnd-pltf-dev-nextflow-scratch-01/work/6a/3a10bbf512dfb1051d2b32e4856c77/HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
  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/5f/7be12205e4476539ddf61e1eb69b3c/.command.run
==> 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: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_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: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_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: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_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: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: HeadNeckN_FFPE_L08_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam.bai
Done