.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bGc-T1-TRNA-1_A23MVY2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/e7de574719b43e3faf21ee99c22cc7/.command.log
Size: 15.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bGc-T1-TRNA-1_A23MVY2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f8/2491441645cfe37989a84a5c0fce92/659_bGc-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cd/88a81337442ba432134f1623a5dda6/659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/e7de574719b43e3faf21ee99c22cc7/.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/8e/340e30ce4f4dec54a95b5e1de8b372/659_bGc-T1-TRNA-1_A23MVY2LT4_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/cf/e7de574719b43e3faf21ee99c22cc7/.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: KIF5B:RET
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: PCDHGB2:PCDHGC4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PCDHA3:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PCDHA3:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: NOTCH2:NBPF11
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_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_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_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_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_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_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_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_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: HSD17B4:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$right),  :
  Ideogram of contig MT cannot be drawn, because no Giemsa staining information is available.
Warning in drawCircos(fusion, fusions, cytobands, minConfidenceForCircosPlot,  :
  Circos plot cannot be drawn, because no Giemsa staining information is available for contig MT.
Drawing fusion #17: HSD17B4:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Warning in drawIdeogram("right", gene2Offset, gene2Offset + max(exons2$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 #18: HSD17B4:MT-RNR2
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.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 #19: ADAMTS12:ADAMTS7P3
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: CLIC2:BX571846.1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: KLRC4:KLRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: KLRC4:KLRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: CLIC2:TMLHE-AS1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: CLIC2:TMLHE-AS1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: PCDHGB2:PCDHGA8
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done