.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/22b5a05b7e7d3fc7af4beb7cea6df2/.command.log
Size: 12.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b7/22b5a05b7e7d3fc7af4beb7cea6df2/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b3/c2cea26fbcf026ea900453b3f47e3a/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ca/a60abc8bba469f1210d001de2a9373/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.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/e4/6802e5b20cb9d64d80ab801507ee46/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.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/b7/22b5a05b7e7d3fc7af4beb7cea6df2/.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: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: PPME1:TCF7L2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: PPME1:TCF7L2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: RBMS1:AFF3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: PTBP3:HSDL2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_1.Aligned.sortedByCoord.out.bam.bai
Done