Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/30/af15205b816de8ba91fc11855d08b8/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/17/0a96b55d84d45d8460e84d472820bc/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/4e69f0b44faf404cb7315252486c98/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/29/c7a87fa19da268b4b93df294774db1/BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/df/4e69f0b44faf404cb7315252486c98/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: BVT_FFPE_TRNA_bld_01_A23WKFTLT4_2.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% (3513962) splicing reads. 164508 splicing junctions. 142040 known splicing junctions. 22468 novel splicing junctions.
sampling 10% (7027924) splicing reads. 182782 splicing junctions. 151210 known splicing junctions. 31572 novel splicing junctions.
sampling 15% (10541886) splicing reads. 191504 splicing junctions. 154901 known splicing junctions. 36603 novel splicing junctions.
sampling 20% (14055848) splicing reads. 196856 splicing junctions. 156965 known splicing junctions. 39891 novel splicing junctions.
sampling 25% (17569810) splicing reads. 200504 splicing junctions. 158289 known splicing junctions. 42215 novel splicing junctions.
sampling 30% (21083772) splicing reads. 203089 splicing junctions. 159154 known splicing junctions. 43935 novel splicing junctions.
sampling 35% (24597734) splicing reads. 205019 splicing junctions. 159829 known splicing junctions. 45190 novel splicing junctions.
sampling 40% (28111696) splicing reads. 206599 splicing junctions. 160379 known splicing junctions. 46220 novel splicing junctions.
sampling 45% (31625658) splicing reads. 207819 splicing junctions. 160745 known splicing junctions. 47074 novel splicing junctions.
sampling 50% (35139620) splicing reads. 208846 splicing junctions. 161071 known splicing junctions. 47775 novel splicing junctions.
sampling 55% (38653582) splicing reads. 209690 splicing junctions. 161325 known splicing junctions. 48365 novel splicing junctions.
sampling 60% (42167544) splicing reads. 210430 splicing junctions. 161531 known splicing junctions. 48899 novel splicing junctions.
sampling 65% (45681506) splicing reads. 211044 splicing junctions. 161689 known splicing junctions. 49355 novel splicing junctions.
sampling 70% (49195468) splicing reads. 211516 splicing junctions. 161813 known splicing junctions. 49703 novel splicing junctions.
sampling 75% (52709430) splicing reads. 211913 splicing junctions. 161919 known splicing junctions. 49994 novel splicing junctions.
sampling 80% (56223392) splicing reads. 212229 splicing junctions. 161996 known splicing junctions. 50233 novel splicing junctions.
sampling 85% (59737354) splicing reads. 212502 splicing junctions. 162056 known splicing junctions. 50446 novel splicing junctions.
sampling 90% (63251316) splicing reads. 212694 splicing junctions. 162098 known splicing junctions. 50596 novel splicing junctions.
sampling 95% (66765278) splicing reads. 212850 splicing junctions. 162134 known splicing junctions. 50716 novel splicing junctions.
sampling 100% (70279240) splicing reads. 212915 splicing junctions. 162147 known splicing junctions. 50768 novel splicing junctions.
null device 
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