.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-4e749e-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/e8eeb2c566f768f6ec0d979cbaf7b9/.command.log
Size: 9.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-4e749e-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9d/e8eeb2c566f768f6ec0d979cbaf7b9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/4801c0c88db67b2c41f79bbdafc351/aih-tih-sc-4e749e-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/94/79f57f62e9b3534ef2a70a6bdc8e05/aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/73ebe6b28cd9f12f59765621def3cd/aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam
  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/9d/e8eeb2c566f768f6ec0d979cbaf7b9/.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: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: GPCPD1:MYO5B
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: ADAMTS2:AC136628.4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_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-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_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-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_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-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_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-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_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-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: GGA3:SLC5A4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: GGA3:SLC5A4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: ADAM9:WRN
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: ADAM9:WRN
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: CHID1:AP2A2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: CHID1:AP2A2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-4e749e-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Done