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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/609b5c48f13434aeb6a40ce553d0b9/.command.log
Size: 15.6 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_eHw-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ff/609b5c48f13434aeb6a40ce553d0b9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9c/8c79adf017d821bd08bea68a584abe/659_eHw-T1-TRNA-1_B23MHV2LT4_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-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/ff/609b5c48f13434aeb6a40ce553d0b9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/45/dd089f36c68689cd614da988470efd/659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3e/1b95d1f13229860c447b8f47566109/659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> 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: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: MYC:CREB3L3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TBP:ATXN3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TBP:ATXN3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: TBP:ATXN3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: TBP:ATXN3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: TBP:ATXN3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: AC092807.3:DDAH1
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: RNF207:ARMH3
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: TMX2:OR9Q1
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #27: ARMH3:ASPH
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_eHw-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done