Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/37/ebb8d66d0e4680eaed709c7ce41c82/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.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/5e/5eff1ff6122a805d876ca9771105ad/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5e/5eff1ff6122a805d876ca9771105ad/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a1/4d20a971c93be1dc46f16704254326/BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BreastNP_FFPE_L02_RNA_01_B23LG7FLT4_1.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% (206932) splicing reads. 57897 splicing junctions. 55899 known splicing junctions. 1998 novel splicing junctions.
sampling 10% (413864) splicing reads. 73820 splicing junctions. 70737 known splicing junctions. 3083 novel splicing junctions.
sampling 15% (620796) splicing reads. 81673 splicing junctions. 77842 known splicing junctions. 3831 novel splicing junctions.
sampling 20% (827729) splicing reads. 86362 splicing junctions. 81993 known splicing junctions. 4369 novel splicing junctions.
sampling 25% (1034661) splicing reads. 89459 splicing junctions. 84623 known splicing junctions. 4836 novel splicing junctions.
sampling 30% (1241593) splicing reads. 91718 splicing junctions. 86516 known splicing junctions. 5202 novel splicing junctions.
sampling 35% (1448526) splicing reads. 93384 splicing junctions. 87892 known splicing junctions. 5492 novel splicing junctions.
sampling 40% (1655458) splicing reads. 94735 splicing junctions. 88989 known splicing junctions. 5746 novel splicing junctions.
sampling 45% (1862390) splicing reads. 95779 splicing junctions. 89788 known splicing junctions. 5991 novel splicing junctions.
sampling 50% (2069323) splicing reads. 96684 splicing junctions. 90486 known splicing junctions. 6198 novel splicing junctions.
sampling 55% (2276255) splicing reads. 97360 splicing junctions. 91015 known splicing junctions. 6345 novel splicing junctions.
sampling 60% (2483187) splicing reads. 97912 splicing junctions. 91430 known splicing junctions. 6482 novel splicing junctions.
sampling 65% (2690119) splicing reads. 98415 splicing junctions. 91801 known splicing junctions. 6614 novel splicing junctions.
sampling 70% (2897052) splicing reads. 98808 splicing junctions. 92073 known splicing junctions. 6735 novel splicing junctions.
sampling 75% (3103984) splicing reads. 99110 splicing junctions. 92296 known splicing junctions. 6814 novel splicing junctions.
sampling 80% (3310916) splicing reads. 99343 splicing junctions. 92470 known splicing junctions. 6873 novel splicing junctions.
sampling 85% (3517849) splicing reads. 99551 splicing junctions. 92613 known splicing junctions. 6938 novel splicing junctions.
sampling 90% (3724781) splicing reads. 99671 splicing junctions. 92698 known splicing junctions. 6973 novel splicing junctions.
sampling 95% (3931713) splicing reads. 99762 splicing junctions. 92765 known splicing junctions. 6997 novel splicing junctions.
sampling 100% (4138646) splicing reads. 99801 splicing junctions. 92791 known splicing junctions. 7010 novel splicing junctions.
null device 
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