.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (KG1_FFPE_01_RNA_0003_B23LG7FLT4_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/e0dfea5727bcef9f2a7816f0e45984/.command.log
Size: 31.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (KG1_FFPE_01_RNA_0003_B23LG7FLT4_3)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ec/2a1f1bc68871f7e126148f546e7976/KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/65/e0dfea5727bcef9f2a7816f0e45984/.command.sh
  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/fc/9da344530526dfb495fcabd4b619b3/KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.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-rnd-pltf-dev-nextflow-scratch-01/work/e6/4940f846f3d5b5aa2231c17340dcaf/KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.FusionInspector.fusions.tsv
  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/65/e0dfea5727bcef9f2a7816f0e45984/.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: FGFR1OP2:FGFR1
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: FGFR1OP2:FGFR1
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: FGFR1OP2:FGFR1
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: RBM14:RBM4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: BCAT1:AC023796.2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: BCAT1:AC023796.2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: GUSBP2:NAIP
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: GUSBP2:NAIP
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: AMN1:WIF1
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: ST7:TFEC
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: ST7:TFEC
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: ST7:TFEC
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: ST7:TFEC
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: PPP1R9A:XRCC2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: PPP1R9A:XRCC2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: CCDC169:SOHLH2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: CCDC169:SOHLH2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #27: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #28: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #29: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #30: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #31: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #32: NPM1:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #33: GRIA3:STAG2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #34: GRIA3:STAG2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #35: PCDHGB2:PCDHGA10
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #36: PCDHGB2:PCDHGA11
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #37: PCDHGB2:PCDHGA12
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #38: PCDHGB2:PCDHGA8
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #39: PCDHGB2:PCDHGA9
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #40: PCDHGB2:PCDHGC3
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #41: PCDHGB2:PCDHGC4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #42: PCDHGB2:PCDHGC5
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #43: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #44: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #45: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #46: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #47: PCDHA4:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #48: PCDHA4:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #49: SMURF2P1:LRRC37B
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #50: SMURF2P1:LRRC37B
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #51: SMURF2P1:LRRC37B
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: KG1_FFPE_01_RNA_0003_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
Done