.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-3a13e9-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/e58e82d8e48fc957924466587e97d8/.command.log
Size: 12.2 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-3a13e9-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/e58e82d8e48fc957924466587e97d8/.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/cf/d25c782ea696c3ae0888709639be4c/aih-tih-sc-3a13e9-R1_A23WJ53LT4_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-rnd-pltf-dev-nextflow-scratch-01/work/3d/f5b03375c22b8c82a4178cc1a4d788/aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  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/37/e58e82d8e48fc957924466587e97d8/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ad/3e2f380cc5a0ed02c16b7cf616bd73/aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.FusionInspector.fusions.tsv
==> 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: TMEM87B:MERTK
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TMEM87B:MERTK
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: NDC1:LDLRAD1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: NDC1:LDLRAD1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TLK2:FAM157A
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TMEM238:BRSK1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TMEM238:BRSK1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: ESR1:CCDC170
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: POLR2J2:FBXL13
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: POLR2J2:FBXL13
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: FSIP1:AC013652.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: FSIP1:AC013652.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-3a13e9-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Done