.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (RGB_RLP_lowDV_1ststrand_42C_3)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/e64a0f91651eae7f6755ed9cae9550/.command.log
Size: 12.9 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (RGB_RLP_lowDV_1ststrand_42C_3)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ee/e64a0f91651eae7f6755ed9cae9550/.command.sh
  Downloading: s3://natera-platform-sandbox/pipeline-resources/AIH/rna/GRCh38/arriba/cytobands_hg38_GRCh38_v2.4.0.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/305f08f086ee736bc1b71d76c3c5a2/RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/78/be9c05f2f1996f23560c3a17192381/RGB_RLP_lowDV_1ststrand_42C_3.FusionInspector.fusions.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/ee/e64a0f91651eae7f6755ed9cae9550/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/60/06719f6b48887043875a4f85056b37/RGB_RLP_lowDV_1ststrand_42C_3.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: SREBF1:NCOR1
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: PCDHA6:PCDHAC1
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PCDHA6:PCDHAC2
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: SRGAP2B:SEC22B3P
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: SUZ12P1:AFMID
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: SUZ12P1:AFMID
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: SUZ12P1:AFMID
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: SUZ12P1:AFMID
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: TVP23C:CDRT4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: GTF2I:CLIP2
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: ASPH:LINC02842
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: ASPH:LINC02842
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: CAB39:ARFIP1
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: METRNL:CTDNEP1
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: LHFPL5:CLPSL1
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: SPATA6:AGBL4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: SPATA6:AGBL4
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: RGB_RLP_lowDV_1ststrand_42C_3.Aligned.sortedByCoord.out.bam.bai
Done