.command.log - Workdir - NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-06a169-R1_A23WJ53LT4_1)

File Info

Filename: .command.log
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/afab2c7f695c639d4f14060aa6bcb9/.command.log
Size: 17.1 KB
Task: NFCORE_RNAFUSION:RNAFUSION:FUSIONINSPECTOR_WORKFLOW:ARRIBA_VISUALISATION (aih-tih-sc-06a169-R1_A23WJ53LT4_1)
Attempt
Content

  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fb/afab2c7f695c639d4f14060aa6bcb9/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6c/8b345b53e7ac042e97ed4582a0f122/aih-tih-sc-06a169-R1_A23WJ53LT4_1.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-rnd-pltf-dev-nextflow-scratch-01/work/bd/b91878d73718e9ad9441d25883b44f/aih-tih-sc-06a169-R1_A23WJ53LT4_1.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/fb/afab2c7f695c639d4f14060aa6bcb9/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bf/dc3aec2566cd6ee505f0009abe4574/aih-tih-sc-06a169-R1_A23WJ53LT4_1.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: TP53:CLDN7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #2: TP53:CLDN7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #3: TP53:CLDN7
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #4: PRPF8:BEST1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #5: PRPF8:BEST1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #6: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #7: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #8: STX16:NPEPL1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #9: TLK2P1:AC110079.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #10: GOLPH3:PDZD2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #11: TLK2:AC240565.1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #12: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #13: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #14: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #15: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #16: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #17: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #18: SH3GLB2:CDC27
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #19: GUCY1B2:NKAIN2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #20: GUCY1B2:NKAIN2
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #21: CHMP4B:LINC02219
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #22: CRYZL2P:SEC16B
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #23: CRYZL2P:SEC16B
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #24: CRYZL2P:SEC16B
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #25: CRYZL2P:SEC16B
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #26: ARHGEF10L:NKAIN1
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #27: SLC39A11:LINC00511
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #28: SLC39A11:LINC00511
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Drawing fusion #29: SLC39A11:LINC00511
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
[W::hts_idx_load3] The index file is older than the data file: aih-tih-sc-06a169-R1_A23WJ53LT4_1.Aligned.sortedByCoord.out.bam.bai
Done