.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-09b6a3-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/406d99acc37de107507bb7adf487db/.command.log
Size: 16.0 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-09b6a3-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/31/406d99acc37de107507bb7adf487db/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f9/547f7454e8f0731900f4490b5f34ee/aih-tih-sc-09b6a3-R1_A23WJ53LT4_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/94/c6b914776742968a7a6f9a3a481803/aih-tih-sc-09b6a3-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-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/31/406d99acc37de107507bb7adf487db/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/41/634be424d910e31b5cd0f516a38eb6/aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
==> 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: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TRPS1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TRPS1:EBAG9
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TRPS1:EBAG9
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: LY6K:TSNARE1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: PVT1:COLEC10
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: PVT1:COLEC10
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: DUT:ANXA2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: DUT:ANXA2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: DUT:ANXA2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: CEP85:CATSPER4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: CEP85:CATSPER4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: GRID1:ADK
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: ATP6V1C1:ZNF280D
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: ATP6V1C1:ZNF280D
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: DOCK1:AZIN1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: ZHX2:COL14A1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: PAPSS2:BLNK
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: MROH1:AC105118.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: MROH1:AC105118.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: NEO1:CSMD3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #27: STK3:PPP1R16A
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-09b6a3-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Done