Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/976a206c506e2bfc1dcdbe9906f9f4/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/f789d11d3dfd58975ba1c1dd754edc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d44def006a04c1e570b58c01359cde/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/73/d44def006a04c1e570b58c01359cde/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/59/865b5c1e28a21171d2f43a3719ea8a/22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 22Rv1_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
reading reference bed file:  ref_annot.bed  ...  Done! Total 386135 known splicing junctions.
Load BAM file ...  Done
shuffling alignments ... Done
sampling 5% (339428) splicing reads. 78715 splicing junctions. 75409 known splicing junctions. 3306 novel splicing junctions.
sampling 10% (678856) splicing reads. 98013 splicing junctions. 92839 known splicing junctions. 5174 novel splicing junctions.
sampling 15% (1018284) splicing reads. 107442 splicing junctions. 100951 known splicing junctions. 6491 novel splicing junctions.
sampling 20% (1357713) splicing reads. 113036 splicing junctions. 105614 known splicing junctions. 7422 novel splicing junctions.
sampling 25% (1697141) splicing reads. 116871 splicing junctions. 108711 known splicing junctions. 8160 novel splicing junctions.
sampling 30% (2036569) splicing reads. 119587 splicing junctions. 110852 known splicing junctions. 8735 novel splicing junctions.
sampling 35% (2375997) splicing reads. 121769 splicing junctions. 112535 known splicing junctions. 9234 novel splicing junctions.
sampling 40% (2715426) splicing reads. 123333 splicing junctions. 113694 known splicing junctions. 9639 novel splicing junctions.
sampling 45% (3054854) splicing reads. 124643 splicing junctions. 114644 known splicing junctions. 9999 novel splicing junctions.
sampling 50% (3394282) splicing reads. 125707 splicing junctions. 115408 known splicing junctions. 10299 novel splicing junctions.
sampling 55% (3733710) splicing reads. 126600 splicing junctions. 116043 known splicing junctions. 10557 novel splicing junctions.
sampling 60% (4073139) splicing reads. 127315 splicing junctions. 116531 known splicing junctions. 10784 novel splicing junctions.
sampling 65% (4412567) splicing reads. 127895 splicing junctions. 116937 known splicing junctions. 10958 novel splicing junctions.
sampling 70% (4751995) splicing reads. 128380 splicing junctions. 117263 known splicing junctions. 11117 novel splicing junctions.
sampling 75% (5091423) splicing reads. 128836 splicing junctions. 117569 known splicing junctions. 11267 novel splicing junctions.
sampling 80% (5430852) splicing reads. 129141 splicing junctions. 117773 known splicing junctions. 11368 novel splicing junctions.
sampling 85% (5770280) splicing reads. 129382 splicing junctions. 117936 known splicing junctions. 11446 novel splicing junctions.
sampling 90% (6109708) splicing reads. 129562 splicing junctions. 118053 known splicing junctions. 11509 novel splicing junctions.
sampling 95% (6449136) splicing reads. 129674 splicing junctions. 118128 known splicing junctions. 11546 novel splicing junctions.
sampling 100% (6788565) splicing reads. 129729 splicing junctions. 118168 known splicing junctions. 11561 novel splicing junctions.
null device 
          1