.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/025dd6243442622c945e6499c9fef5/.command.log
Size: 7.4 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/aa/ad00d91b871c77c26e40f9a6b6b84d/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/025dd6243442622c945e6499c9fef5/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/90/6ae1b7a15d34f62dce429a4639b223/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.FusionInspector.fusions.tsv
  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/fe/025dd6243442622c945e6499c9fef5/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f7/9b2a39216732e94a63b9c756b6e117/1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
==> 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: ITCH:PHF20
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: PAN3:POLR1D
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: SCX:MROH1
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: SCX:MROH1
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: INPP5A:AL596223.1
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: INPP5A:AL596223.1
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: INPP5A:AL596223.1
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 1173_F0Y_T1_RNA_SLD_01_A23T55JLT4_2.Aligned.sortedByCoord.out.bam.bai
Done