.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (rna_s1221_S42)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/fa860c169fe900d5615baf70d47ed1/.command.log
Size: 6.8 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (rna_s1221_S42)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/72/f2dd814cb66b27bad1201ee907daea/rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8c/fa860c169fe900d5615baf70d47ed1/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/03/3c84dec72e4bcedf67661807e217ae/rna_s1221_S42.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0f/990b4031093ebd9df29b044a20adaa/rna_s1221_S42.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/8c/fa860c169fe900d5615baf70d47ed1/.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: FGFR3:TACC3
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: LMNA:NTRK1
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: PAX8:PPARG
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: ETV6:NTRK3
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: EGFR:SEPTIN14
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: FGFR3:BAIAP2L1
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: KIF5B:RET
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: CD74:ROS1
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: NCOA4:RET
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: AC015911.9:SLFN12L
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: AC015911.9:SLFN12L
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: SLC45A3:BRAF
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1221_S42.Aligned.sortedByCoord.out.bam.bai
Done