.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_epZ-T1-TRNA-1_B23MHV2LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/ba4490ae7ceff322ced5518308d4da/.command.log
Size: 8.7 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_epZ-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b6/06fd18017e7b36d58841010eb75b4e/659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/425be8caec576e8fc5fff9141398b1/659_epZ-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/ba4490ae7ceff322ced5518308d4da/.command.sh
  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/0d/ba4490ae7ceff322ced5518308d4da/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/ec1b2b60f200fcfea3a4b1a3241d0b/659_epZ-T1-TRNA-1_B23MHV2LT4_1.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: ATF1:EWSR1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: EWSR1:ATF1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PCDHA10:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PCDHA10:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: PCDHA10:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: PCDHA10:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: PCDHA10:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: PCDHA10:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: RPN2:SPATA5
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: RPN2:SPATA5
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: UBR4:MINDY3
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: UBR4:MINDY3
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: MINDY3:UBR4
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: RNF216:EIF2AK1
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_epZ-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done