.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_6i-T1-TRNA-1_A23MVY2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/bdb481c9a2224a27a5e089c98d13cd/.command.log
Size: 15.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_6i-T1-TRNA-1_A23MVY2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d4/bdb481c9a2224a27a5e089c98d13cd/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/94f87efce0c9ea1070184b2035b932/659_6i-T1-TRNA-1_A23MVY2LT4_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-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/d4/bdb481c9a2224a27a5e089c98d13cd/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/46/b0b0e9776ae6d46e7e6f0e6fbfd54c/659_6i-T1-TRNA-1_A23MVY2LT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5c/0a873d9884b3f2d94f5fca36ab3aa5/659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
==> 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: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TMPRSS2:ERG
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: CPNE4:ADGRG7
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_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_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: DAPK2:RAD51B
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: PCDHA4:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: PCDHA4:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: ARL13B:AC021055.1
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_6i-T1-TRNA-1_A23MVY2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done