.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/06c250027c8da106a0eabc6a16986a/.command.log
Size: 8.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/06c250027c8da106a0eabc6a16986a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/7ba4a71cca83f6facee8a0767ba77f/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
  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/0a/fbb5b8944dcd5948b7bab7b5e40712/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.FusionInspector.fusions.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/33/06c250027c8da106a0eabc6a16986a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/e7/55ba7cb76d62f563f9e9f01f19fdf8/BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.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: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PCDHA4:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: PCDHA4:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: MSI2:CLTC
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: EXOC2:EPHA5
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: RIC1:FMNL1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: GUSB:NAIP
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: C22orf39:MYO18B-AS1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: C22orf39:MYO18B-AS1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: SHMT2:RACGAP1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_01_A23WKFTLT4_3.Aligned.sortedByCoord.out.bam.bai
Done