.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-505123-R1_B23WHYVLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/e53da952cd9febc70aff6eec238a97/.command.log
Size: 14.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-505123-R1_B23WHYVLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d5/e53da952cd9febc70aff6eec238a97/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/97/28e787add1773c6f47ee3119fb786f/aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5b/89059edb6611088a3d176434796e0f/aih-tih-sc-505123-R1_B23WHYVLT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cc/a09e61136c259d28b3f82367af7c0c/aih-tih-sc-505123-R1_B23WHYVLT4_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/d5/e53da952cd9febc70aff6eec238a97/.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: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: PTPN20:BMS1P7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: RASA4:POLR2J2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: PCDHGB2:PCDHGA10
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: PCDHGB2:PCDHGA11
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: PCDHGB2:PCDHGA12
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: PCDHGB2:PCDHGA8
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: PCDHGB2:PCDHGA9
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: PCDHGB2:PCDHGC3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: PCDHGB2:PCDHGC4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: PCDHGB2:PCDHGC5
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: PCDHA6:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: PCDHA6:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-505123-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Done