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

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/a931ff12bff194922833aa1971726e/.command.log
Size: 14.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (659_bGc-T1-TRNA-1_B23MHV2LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/ce342ec72a56a63b3c624087e67a95/659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b8/a931ff12bff194922833aa1971726e/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/b9/aaf3ee6440e03466793c61c0189e9f/659_bGc-T1-TRNA-1_B23MHV2LT4_1.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/23/9742a23f2a3c7761b1ce7d9ad23ac5/659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  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/b8/a931ff12bff194922833aa1971726e/.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: KIF5B:RET
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: KIF5B:RET
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PCDHGB2:PCDHGC4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PCDHGB2:PCDHGA10
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: NOTCH2:NBPF11
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: GUSBP2:NAIP
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: GUSBP2:NAIP
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: TLK2:LINC01002
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: CLIC2:TMLHE-AS1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: CLIC2:TMLHE-AS1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: KLRC4:KLRK1
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: PTMS:MTRNR2L8
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: 659_bGc-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
Done