Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/3a/93a632584eb29d4b8e07d0fdb1e313/659_bTq-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam.bai
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/ce/ead7548c923424c68495c616845975/ref_annot.bed
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/7e3fa0ceeffd6be59d25a5aaed855a/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/dc/7e3fa0ceeffd6be59d25a5aaed855a/.command.run
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/6e/5095ca24cc799e6d6e75cacc570c6b/659_bTq-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_bTq-T1-TRNA-1_B23MHV2LT4_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% (16525886) splicing reads. 273975 splicing junctions. 190874 known splicing junctions. 83101 novel splicing junctions.
sampling 10% (33051772) splicing reads. 337977 splicing junctions. 204114 known splicing junctions. 133863 novel splicing junctions.
sampling 15% (49577659) splicing reads. 384684 splicing junctions. 211455 known splicing junctions. 173229 novel splicing junctions.
sampling 20% (66103545) splicing reads. 421797 splicing junctions. 216294 known splicing junctions. 205503 novel splicing junctions.
sampling 25% (82629432) splicing reads. 453443 splicing junctions. 219950 known splicing junctions. 233493 novel splicing junctions.
sampling 30% (99155318) splicing reads. 480778 splicing junctions. 222778 known splicing junctions. 258000 novel splicing junctions.
sampling 35% (115681204) splicing reads. 504553 splicing junctions. 225000 known splicing junctions. 279553 novel splicing junctions.
sampling 40% (132207091) splicing reads. 525640 splicing junctions. 226861 known splicing junctions. 298779 novel splicing junctions.
sampling 45% (148732977) splicing reads. 544508 splicing junctions. 228448 known splicing junctions. 316060 novel splicing junctions.
sampling 50% (165258864) splicing reads. 561393 splicing junctions. 229726 known splicing junctions. 331667 novel splicing junctions.
sampling 55% (181784750) splicing reads. 576818 splicing junctions. 230815 known splicing junctions. 346003 novel splicing junctions.
sampling 60% (198310636) splicing reads. 590590 splicing junctions. 231776 known splicing junctions. 358814 novel splicing junctions.
sampling 65% (214836523) splicing reads. 602899 splicing junctions. 232646 known splicing junctions. 370253 novel splicing junctions.
sampling 70% (231362409) splicing reads. 613805 splicing junctions. 233404 known splicing junctions. 380401 novel splicing junctions.
sampling 75% (247888296) splicing reads. 623802 splicing junctions. 234068 known splicing junctions. 389734 novel splicing junctions.
sampling 80% (264414182) splicing reads. 632657 splicing junctions. 234663 known splicing junctions. 397994 novel splicing junctions.
sampling 85% (280940068) splicing reads. 640514 splicing junctions. 235156 known splicing junctions. 405358 novel splicing junctions.
sampling 90% (297465955) splicing reads. 647403 splicing junctions. 235549 known splicing junctions. 411854 novel splicing junctions.
sampling 95% (313991841) splicing reads. 653343 splicing junctions. 235919 known splicing junctions. 417424 novel splicing junctions.
sampling 100% (330517728) splicing reads. 658559 splicing junctions. 236233 known splicing junctions. 422326 novel splicing junctions.
null device 
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