.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bua-T1-TRNA-1_B23WHTKLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/47e78ab7b82f445cb823cfcf45ae38/.command.log
Size: 11.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bua-T1-TRNA-1_B23WHTKLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4d/47e78ab7b82f445cb823cfcf45ae38/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/425fbf5ce7bb2fa3d66c7b64e48711/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/36/faf4df8f2d11bdefd5dd839c878af7/659_bua-T1-TRNA-1_B23WHTKLT4_1.FusionInspector.fusions.tsv
  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/f6/9d130904f6d70eb1f8a2d201078066/659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam
  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/4d/47e78ab7b82f445cb823cfcf45ae38/.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: TPM3:NTRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TPM3:NTRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TPM3:NTRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TPM3:NTRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: RARS1:WWC1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: RARS1:WWC1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: RARS1:WWC1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: CRACD:THEGL
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: CRACD:THEGL
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: CRACD:THEGL
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: CRACD:THEGL
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: ADAMTS2:RARS1
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bua-T1-TRNA-1_B23WHTKLT4_1.Aligned.sortedByCoord.out.bam.bai
Done