Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/d7/45b4611e0e84f1398fa97b4879d974/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/58/ffcae09cb11657715a509b26115a7f/A549_FFPE_01_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/56/13a0da7a90913d31925104f03d721b/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/587347ad3b089bd3f067a5ceabe282/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/8e/587347ad3b089bd3f067a5ceabe282/.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. 25 splicing junctions. 6 known splicing junctions. 19 novel splicing junctions.
sampling 10% (92) splicing reads. 38 splicing junctions. 8 known splicing junctions. 30 novel splicing junctions.
sampling 15% (138) splicing reads. 46 splicing junctions. 9 known splicing junctions. 37 novel splicing junctions.
sampling 20% (184) splicing reads. 55 splicing junctions. 11 known splicing junctions. 44 novel splicing junctions.
sampling 25% (230) splicing reads. 61 splicing junctions. 12 known splicing junctions. 49 novel splicing junctions.
sampling 30% (276) splicing reads. 67 splicing junctions. 12 known splicing junctions. 55 novel splicing junctions.
sampling 35% (323) splicing reads. 71 splicing junctions. 12 known splicing junctions. 59 novel splicing junctions.
sampling 40% (369) splicing reads. 77 splicing junctions. 12 known splicing junctions. 65 novel splicing junctions.
sampling 45% (415) splicing reads. 83 splicing junctions. 13 known splicing junctions. 70 novel splicing junctions.
sampling 50% (461) splicing reads. 89 splicing junctions. 13 known splicing junctions. 76 novel splicing junctions.
sampling 55% (507) splicing reads. 92 splicing junctions. 13 known splicing junctions. 79 novel splicing junctions.
sampling 60% (553) splicing reads. 93 splicing junctions. 13 known splicing junctions. 80 novel splicing junctions.
sampling 65% (599) splicing reads. 93 splicing junctions. 13 known splicing junctions. 80 novel splicing junctions.
sampling 70% (646) splicing reads. 96 splicing junctions. 13 known splicing junctions. 83 novel splicing junctions.
sampling 75% (692) splicing reads. 99 splicing junctions. 13 known splicing junctions. 86 novel splicing junctions.
sampling 80% (738) splicing reads. 99 splicing junctions. 13 known splicing junctions. 86 novel splicing junctions.
sampling 85% (784) splicing reads. 102 splicing junctions. 13 known splicing junctions. 89 novel splicing junctions.
sampling 90% (830) splicing reads. 103 splicing junctions. 13 known splicing junctions. 90 novel splicing junctions.
sampling 95% (876) splicing reads. 105 splicing junctions. 13 known splicing junctions. 92 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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