.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (rna_s1200_S21)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/2b30ecb33e36fc2eb225de90f54f12/.command.log
Size: 4.5 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (rna_s1200_S21)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ed/5aff5498f315e9353e31d30d17b123/rna_s1200_S21.FusionInspector.fusions.tsv
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/26/2b30ecb33e36fc2eb225de90f54f12/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/1c/320c77402664fc25775a7c2675bb8d/rna_s1200_S21.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-rnd-pltf-dev-nextflow-scratch-01/work/26/2b30ecb33e36fc2eb225de90f54f12/.command.run
  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/e8/613d27af2da60f89ec407c24b98028/rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
==> 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_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: LMNA:NTRK1
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: FGFR3:BAIAP2L1
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: ETV6:NTRK3
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: CD74:ROS1
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: KIF5B:RET
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: PAX8:PPARG
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: rna_s1200_S21.Aligned.sortedByCoord.out.bam.bai
Done