Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9b/fe551878c91538d7946d2502e6cdf1/659_1q-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/0d/6dc89be5daa0feb029591819578261/659_1q-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/06/146553381f3c7948f6876a6e229ef0/.command.sh
  Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/06/146553381f3c7948f6876a6e229ef0/.command.run
==> STAGING COMPLETE (5 inputs)

[W::hts_idx_load3] The index file is older than the data file: 659_1q-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% (15811381) splicing reads. 260863 splicing junctions. 179811 known splicing junctions. 81052 novel splicing junctions.
sampling 10% (31622763) splicing reads. 323776 splicing junctions. 193134 known splicing junctions. 130642 novel splicing junctions.
sampling 15% (47434144) splicing reads. 369330 splicing junctions. 200462 known splicing junctions. 168868 novel splicing junctions.
sampling 20% (63245526) splicing reads. 405714 splicing junctions. 205434 known splicing junctions. 200280 novel splicing junctions.
sampling 25% (79056907) splicing reads. 436389 splicing junctions. 209058 known splicing junctions. 227331 novel splicing junctions.
sampling 30% (94868289) splicing reads. 462507 splicing junctions. 211848 known splicing junctions. 250659 novel splicing junctions.
sampling 35% (110679670) splicing reads. 485099 splicing junctions. 214011 known splicing junctions. 271088 novel splicing junctions.
sampling 40% (126491052) splicing reads. 504982 splicing junctions. 215879 known splicing junctions. 289103 novel splicing junctions.
sampling 45% (142302433) splicing reads. 522714 splicing junctions. 217366 known splicing junctions. 305348 novel splicing junctions.
sampling 50% (158113815) splicing reads. 538195 splicing junctions. 218630 known splicing junctions. 319565 novel splicing junctions.
sampling 55% (173925197) splicing reads. 552133 splicing junctions. 219746 known splicing junctions. 332387 novel splicing junctions.
sampling 60% (189736578) splicing reads. 564458 splicing junctions. 220650 known splicing junctions. 343808 novel splicing junctions.
sampling 65% (205547960) splicing reads. 575548 splicing junctions. 221428 known splicing junctions. 354120 novel splicing junctions.
sampling 70% (221359341) splicing reads. 585259 splicing junctions. 222130 known splicing junctions. 363129 novel splicing junctions.
sampling 75% (237170723) splicing reads. 593852 splicing junctions. 222795 known splicing junctions. 371057 novel splicing junctions.
sampling 80% (252982104) splicing reads. 601409 splicing junctions. 223333 known splicing junctions. 378076 novel splicing junctions.
sampling 85% (268793486) splicing reads. 608005 splicing junctions. 223786 known splicing junctions. 384219 novel splicing junctions.
sampling 90% (284604867) splicing reads. 613579 splicing junctions. 224151 known splicing junctions. 389428 novel splicing junctions.
sampling 95% (300416249) splicing reads. 618234 splicing junctions. 224477 known splicing junctions. 393757 novel splicing junctions.
sampling 100% (316227631) splicing reads. 621945 splicing junctions. 224722 known splicing junctions. 397223 novel splicing junctions.
null device 
          1