.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (GM24385_0001_RNA_0001_23H5VFLT4_s24)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/3b71aa74545fc2dac33a0fc767b17b/.command.log
Size: 6.3 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (GM24385_0001_RNA_0001_23H5VFLT4_s24)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/55/3b71aa74545fc2dac33a0fc767b17b/.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/de/a361851e75629faef8a9cf2d392fc5/GM24385_0001_RNA_0001_23H5VFLT4_s24.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-rnd-pltf-dev-nextflow-scratch-01/work/98/cb5c4b183349561367b746d2c6cdd5/GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/ed96f47b21142c700e79fd65d25490/GM24385_0001_RNA_0001_23H5VFLT4_s24.FusionInspector.fusions.tsv
  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/55/3b71aa74545fc2dac33a0fc767b17b/.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: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: GM24385_0001_RNA_0001_23H5VFLT4_s24.Aligned.sortedByCoord.out.bam.bai
Done