.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-45523c-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/08652ee3b1cda8269287ed6eedd920/.command.log
Size: 13.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-45523c-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ea/08652ee3b1cda8269287ed6eedd920/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a3/522c15b90a488b29f43d20e3578c35/aih-tih-sc-45523c-R1_A23YTGFLT4_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-rnd-pltf-dev-nextflow-scratch-01/work/35/9046ff9a18fb2775abaab1c2fa435e/aih-tih-sc-45523c-R1_A23YTGFLT4_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/ea/08652ee3b1cda8269287ed6eedd920/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/bacb5ddad45aa89e83a2f8717ba1a2/aih-tih-sc-45523c-R1_A23YTGFLT4_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: KIAA1958:NTRK2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: KIAA1958:NTRK2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PCDHA11:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PCDHA11:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_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-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_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-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_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-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_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: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: DDX5:SMURF2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: FSIP1:AC013652.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: FSIP1:AC013652.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_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-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: ZFHX3:CNTNAP4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: ERC1:RASSF7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: ERC1:RASSF7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: WWP2:MPHOSPH6
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-45523c-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Done