File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/28dcfe280ec17d8bdb7580452fe0ee/.command.log
Size
4.0 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (GM24385_0001_RNA_0001_23H5VFLT4_s32)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/24/28dcfe280ec17d8bdb7580452fe0ee/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/20/03cfc4207eb002aeb18f46e1cc3627/GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/01dffac13eb895a93a69073bb41be5/GM24385_0001_RNA_0001_23H5VFLT4_s32.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/35/06ef061c7b0f9e35e21bb93e492047/GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
  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/24/28dcfe280ec17d8bdb7580452fe0ee/.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: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s32.Aligned.sortedByCoord.out.bam.bai
Done