File Info

Filename
.command.log
Full Path
s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/cf85ad0160061880255512ae9aadc1/.command.log
Size
13.5 KB
Task
NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2)
Attempt

Content

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  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/40/cf85ad0160061880255512ae9aadc1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f0/e7fe4b48f817cfc84e2177bbff47fd/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
  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/40/cf85ad0160061880255512ae9aadc1/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/f4dd92f7917b43da4087ed6809a2e0/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/de/f758e671ab576f3b93b2d94f1ed304/BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.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: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: NARS2:GAB2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: PCDHA4:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: PCDHA4:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: EXOC2:EPHA5
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: EXOC2:EPHA5
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: RIC1:FMNL1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: MSI2:CLTC
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: AC092070.2:MAN2B1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: AC092070.2:MAN2B1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: GUSB:NAIP
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: ZSCAN22:WWC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: ZSCAN22:WWC3
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: SHMT2:RACGAP1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: C22orf39:MYO18B-AS1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: C22orf39:MYO18B-AS1
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bst_01_02_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
Done