Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/2c/790475faea7a2d0e4e536f771ee218/.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/1d/2934170822e99530ff94cb270f4b05/659_bCu-T1-TRNA-1_B23MHV2LT4_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/2c/790475faea7a2d0e4e536f771ee218/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/44/3d1ebd263a82617d9e3d8c7abb1640/659_bCu-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/a30572dea4a112632006769b028dca/659_bCu-T1-TRNA-1_B23MHV2LT4_1.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: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TNS1:ALK
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: NAV2:NELL1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: NAV2:NELL1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: NAV2:NELL1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: NAV2:NELL1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: IRAG1:ZNF143
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: IRAG1:ZNF143
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: IRAG1:ZNF143
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: TRPC2:WEE1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: TRPC2:WEE1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: TRPC2:WEE1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: PPFIBP2:PARVA
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: PPFIBP2:PARVA
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: PPFIBP2:PARVA
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: ADAM23:HDAC4
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: ADAM23:HDAC4
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: RHOG:SBF2
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: RHOG:SBF2
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #27: PCDHA10:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #28: PCDHA10:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #29: HDAC4:KCNS3
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #30: ZNF143:LINC02751
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bCu-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done