Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0e/ea93e46da6bd582932d770dbd03bfe/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/52/7bea65e4c47222751705f286fe452b/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
  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/bb/767c7c64e0f4c63b31fb5934b9e9da/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/bb/767c7c64e0f4c63b31fb5934b9e9da/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: A549_FFPE_01_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% (46) splicing reads. 18 splicing junctions. 4 known splicing junctions. 14 novel splicing junctions.
sampling 10% (92) splicing reads. 33 splicing junctions. 7 known splicing junctions. 26 novel splicing junctions.
sampling 15% (138) splicing reads. 43 splicing junctions. 7 known splicing junctions. 36 novel splicing junctions.
sampling 20% (184) splicing reads. 53 splicing junctions. 7 known splicing junctions. 46 novel splicing junctions.
sampling 25% (230) splicing reads. 62 splicing junctions. 8 known splicing junctions. 54 novel splicing junctions.
sampling 30% (276) splicing reads. 70 splicing junctions. 8 known splicing junctions. 62 novel splicing junctions.
sampling 35% (323) splicing reads. 78 splicing junctions. 8 known splicing junctions. 70 novel splicing junctions.
sampling 40% (369) splicing reads. 81 splicing junctions. 8 known splicing junctions. 73 novel splicing junctions.
sampling 45% (415) splicing reads. 84 splicing junctions. 8 known splicing junctions. 76 novel splicing junctions.
sampling 50% (461) splicing reads. 86 splicing junctions. 8 known splicing junctions. 78 novel splicing junctions.
sampling 55% (507) splicing reads. 88 splicing junctions. 8 known splicing junctions. 80 novel splicing junctions.
sampling 60% (553) splicing reads. 93 splicing junctions. 9 known splicing junctions. 84 novel splicing junctions.
sampling 65% (599) splicing reads. 94 splicing junctions. 9 known splicing junctions. 85 novel splicing junctions.
sampling 70% (646) splicing reads. 96 splicing junctions. 11 known splicing junctions. 85 novel splicing junctions.
sampling 75% (692) splicing reads. 99 splicing junctions. 12 known splicing junctions. 87 novel splicing junctions.
sampling 80% (738) splicing reads. 101 splicing junctions. 13 known splicing junctions. 88 novel splicing junctions.
sampling 85% (784) splicing reads. 103 splicing junctions. 13 known splicing junctions. 90 novel splicing junctions.
sampling 90% (830) splicing reads. 104 splicing junctions. 13 known splicing junctions. 91 novel splicing junctions.
sampling 95% (876) splicing reads. 104 splicing junctions. 13 known splicing junctions. 91 novel splicing junctions.
sampling 100% (923) splicing reads. 105 splicing junctions. 13 known splicing junctions. 92 novel splicing junctions.
null device 
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