.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/13b96d946d6c422d49f1d03ee26d5f/.command.log
Size: 7.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cf/f23bb31e470587dfe008557f43d6da/aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/13b96d946d6c422d49f1d03ee26d5f/.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/0a/84d5298bf3cdd9fa97f7a8bf8c8dec/aih-tih-sc-2b9bfa-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/6e/13b96d946d6c422d49f1d03ee26d5f/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/9418e91c58aeed5ff609ea3ad9b8af/aih-tih-sc-2b9bfa-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: SRRM1:CLIC4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_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-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-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-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-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-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: DTX2:PTPN12
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: KLRC4:KLRK1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-2b9bfa-R1_A23YTGFLT4_1.Aligned.sortedByCoord.out.bam.bai
Done