.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-60f9b9-R1_B23WHYVLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/4836957a24e8b458d1a95eff3a2a0c/.command.log
Size: 8.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-60f9b9-R1_B23WHYVLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/b6be89615b6795f000200a1b7f3785/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3b/4836957a24e8b458d1a95eff3a2a0c/.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/70/c5841d99fc1a6565698b0a86c4fa01/aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/33/99397c4aa00d8cf01cbb0a9f5158a5/aih-tih-sc-60f9b9-R1_B23WHYVLT4_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/3b/4836957a24e8b458d1a95eff3a2a0c/.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: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: SSH2:NF1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_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-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_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-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_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-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: IGF1R:PHF24
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: CSDE1:STRIP1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: CSDE1:STRIP1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: MELK:RGS3
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-60f9b9-R1_B23WHYVLT4_1.Aligned.sortedByCoord.out.bam.bai
Done