Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/ce032bfbb3cf0e48caf22f2f664f76/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/fe/c82e10e1f775b5e770785b1bfc3423/786-O_FFPE_RNA_0001_B23LG7FLT4_3.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/4a/ce032bfbb3cf0e48caf22f2f664f76/.command.run
==> STAGING COMPLETE (3 inputs)
PAIRED_END_BAM_INPUT
Processed 1000000 records
Processed 2000000 records
Processed 3000000 records
Processed 4000000 records
Processed 5000000 records
Processed 6000000 records
Processed 7000000 records
Processed 8000000 records
Processed 9000000 records
Processed 10000000 records
Processed 11000000 records
Processed 12000000 records
Processed 13000000 records
Processed 14000000 records
Processed 15000000 records
Processed 16000000 records
Processed 17000000 records
Processed 18000000 records
Processed 19000000 records
Processed 20000000 records
Processed 21000000 records
Processed 22000000 records
Processed 23000000 records
Processed 24000000 records
Processed 25000000 records
Processed 26000000 records
Processed 27000000 records
Processed 28000000 records
Processed 29000000 records
Processed 30000000 records
Processed 31000000 records
Processed 32000000 records
Processed 33000000 records
Processed 34000000 records
Processed 35000000 records
Processed 36000000 records
Processed 37000000 records
Processed 38000000 records
Processed 39000000 records
Processed 40000000 records
Processed 41000000 records
Processed 42000000 records
Processed 43000000 records
Processed 44000000 records
Processed 45000000 records
Processed 46000000 records
Processed 47000000 records
Processed 48000000 records
Processed 49000000 records
Processed 50000000 records
Processed 51000000 records
Processed 52000000 records
Processed 53000000 records
Processed 54000000 records
Processed 55000000 records
Processed 56000000 records
Processed 57000000 records
Processed 58000000 records
Processed 59000000 records
Processed 60000000 records
Processed 61000000 records
Processed 62000000 records
Processed 63000000 records
Processed 64000000 records
Processed 65000000 records
Processed 66000000 records
Processed 67000000 records
Processed 68000000 records
Processed 69000000 records
Processed 70000000 records
Processed 71000000 records
Processed 72000000 records
Processed 73000000 records
Processed 74000000 records
Processed 75000000 records
Processed 76000000 records
Processed 77000000 records
Processed 78000000 records
Processed 79000000 records
Processed 80000000 records
Processed 81000000 records
Processed 82000000 records
Processed 83000000 records
Processed 84000000 records
Processed 85000000 records
Processed 86000000 records
Processed 87000000 records
Processed 88000000 records
Processed 89000000 records
Processed 90000000 records
Processed 91000000 records
Processed 92000000 records
Processed 93000000 records
Processed 94000000 records
Processed 95000000 records
Processed 96000000 records
Processed 97000000 records
Processed 98000000 records
Processed 99000000 records
Processed 100000000 records
Processed 101000000 records
Processed 102000000 records
Processed 103000000 records
Processed 104000000 records
Processed 105000000 records
Processed 106000000 records
Processed 107000000 records
Processed 108000000 records
Processed 109000000 records
Processed 110000000 records
Processed 111000000 records
Processed 112000000 records
Processed 113000000 records
Processed 114000000 records
Processed 115000000 records
Processed 116000000 records
Processed 117000000 records
Processed 118000000 records
Processed 119000000 records
Processed 120000000 records
Processed 121000000 records
Processed 122000000 records
Processed 123000000 records
Processed 124000000 records
Processed 125000000 records
Processed 126000000 records
Processed 127000000 records
Processed 128000000 records
Processed 129000000 records
Processed 130000000 records
Processed 131000000 records
Processed 132000000 records
Processed 133000000 records
Processed 134000000 records
Processed 135000000 records
Processed 136000000 records
Processed 137000000 records
Processed 138000000 records
Processed 139000000 records
Processed 140000000 records
Processed 141000000 records
Processed 142000000 records
Processed 143000000 records
Processed 144000000 records
Processed 145000000 records
Processed 146000000 records
Processed 147000000 records
Processed 148000000 records
Processed 149000000 records
Processed 150000000 records
Processed 151000000 records
Processed 152000000 records
Processed 153000000 records
Processed 154000000 records
Processed 155000000 records
Processed 156000000 records
Processed 157000000 records
Processed 158000000 records
Processed 159000000 records
Processed 160000000 records
Processed 161000000 records
Processed 162000000 records
Processed 163000000 records
Processed 164000000 records
Processed 165000000 records
Processed 166000000 records
Processed 167000000 records
Processed 168000000 records
Processed 169000000 records
Processed 170000000 records
Processed 171000000 records
Processed 172000000 records
Processed 173000000 records
Processed 174000000 records
Processed 175000000 records
Processed 176000000 records
Processed 177000000 records
Processed 178000000 records
Processed 179000000 records
Processed 180000000 records
Processed 181000000 records
Processed 182000000 records
Processed 183000000 records
Processed 184000000 records
Processed 185000000 records
Processed 186000000 records
Processed 187000000 records
Processed 188000000 records
Processed 189000000 records
Processed 190000000 records
Processed 191000000 records
Processed 192000000 records
Processed 193000000 records
Processed 194000000 records
Processed 195000000 records
Processed 196000000 records
Processed 197000000 records
Processed 198000000 records
Processed 199000000 records
Processed 200000000 records
Processed 201000000 records
Processed 202000000 records
Processed 203000000 records
Processed 204000000 records
Processed 205000000 records
Processed 206000000 records
Processed 207000000 records
Processed 208000000 records
Processed 209000000 records
Processed 210000000 records
Processed 211000000 records
Processed 212000000 records
Processed 213000000 records
Processed 214000000 records
Processed 215000000 records
Processed 216000000 records
Processed 217000000 records
Processed 218000000 records
Processed 219000000 records
Processed 220000000 records
Processed 221000000 records
Processed 222000000 records
Processed 223000000 records
Processed 224000000 records
Processed 225000000 records
Processed 226000000 records
Processed 227000000 records
Processed 228000000 records
Processed 229000000 records
Processed 230000000 records
Processed 231000000 records
Processed 232000000 records
Processed 233000000 records
Processed 234000000 records
Processed 235000000 records
Processed 236000000 records
Processed 237000000 records
Processed 238000000 records
Processed 239000000 records
Processed 240000000 records
Processed 241000000 records
Processed 242000000 records
Processed 243000000 records
Processed 244000000 records
Processed 245000000 records
Processed 246000000 records
Processed 247000000 records
Processed 248000000 records
Processed 249000000 records
Processed 250000000 records
Processed 251000000 records
Processed 252000000 records
Processed 253000000 records
Processed 254000000 records
Processed 255000000 records
Processed 256000000 records
Processed 257000000 records
Processed 258000000 records
Processed 259000000 records
Processed 260000000 records
Processed 261000000 records
Processed 262000000 records
Processed 263000000 records
Processed 264000000 records
Processed 265000000 records
Processed 266000000 records
Processed 267000000 records
Processed 268000000 records
Processed 269000000 records
Processed 270000000 records
Processed 271000000 records
Processed 272000000 records
Processed 273000000 records
Processed 274000000 records
Processed 275000000 records
Processed 276000000 records
Processed 277000000 records
Processed 278000000 records
Processed 279000000 records
Processed 280000000 records
Processed 281000000 records
Processed 282000000 records
Processed 283000000 records
Processed 284000000 records
Processed 285000000 records
Processed 286000000 records
Processed 287000000 records
Processed 288000000 records
Processed 289000000 records
Processed 290000000 records
Processed 291000000 records
Processed 292000000 records
Processed 293000000 records
Processed 294000000 records
Processed 295000000 records
Processed 296000000 records
Processed 297000000 records
Processed 298000000 records
Processed 299000000 records
Processed 300000000 records
Processed 301000000 records
Processed 302000000 records
Processed 303000000 records
Processed 304000000 records
Processed 305000000 records
Processed 306000000 records
Processed 307000000 records
Processed 308000000 records
Processed 309000000 records
Processed 310000000 records
Processed 311000000 records
Processed 312000000 records
Processed 313000000 records
Processed 314000000 records
Processed 315000000 records
Processed 316000000 records
Processed 317000000 records
Processed 318000000 records
Processed 319000000 records
Processed 320000000 records
Processed 321000000 records
Processed 322000000 records
Processed 323000000 records
Processed 324000000 records
Processed 325000000 records
Processed 326000000 records
Processed 327000000 records
Processed 328000000 records
Processed 329000000 records
Processed 330000000 records
Processed 331000000 records
Processed 332000000 records
Processed 333000000 records
Processed 334000000 records
Processed 335000000 records
Processed 336000000 records
Processed 337000000 records
Processed 338000000 records
Processed 339000000 records
Processed 340000000 records
Processed 341000000 records
Processed 342000000 records
Processed 343000000 records
Processed 344000000 records
Processed 345000000 records
Processed 346000000 records
Processed 347000000 records
Processed 348000000 records
Processed 349000000 records
Processed 350000000 records
Processed 351000000 records
Processed 352000000 records
Processed 353000000 records
Processed 354000000 records
Processed 355000000 records
Processed 356000000 records
Processed 357000000 records
Processed 358000000 records
Processed 359000000 records
Processed 360000000 records
Processed 361000000 records
Processed 362000000 records
Processed 363000000 records
Processed 364000000 records
Processed 365000000 records
Processed 366000000 records
Processed 367000000 records
Processed 368000000 records
Processed 369000000 records
Processed 370000000 records
Processed 371000000 records
Processed 372000000 records
Processed 373000000 records
Processed 374000000 records
Processed 375000000 records
Processed 376000000 records
Processed 377000000 records
Processed 378000000 records
Processed 379000000 records
Processed 380000000 records
Processed 381000000 records
Processed 382000000 records
Processed 383000000 records
Processed 384000000 records
Processed 385000000 records
Processed 386000000 records
Processed 387000000 records
Processed 388000000 records
Processed 389000000 records
Processed 390000000 records
Processed 391000000 records
Processed 392000000 records
Processed 393000000 records
Processed 394000000 records
Processed 395000000 records
Processed 396000000 records
Processed 397000000 records
Processed 398000000 records
Processed 399000000 records
Processed 400000000 records
Processed 401000000 records
Processed 402000000 records
Processed 403000000 records
Processed 404000000 records
Processed 405000000 records
Processed 406000000 records
Processed 407000000 records
Processed 408000000 records
Processed 409000000 records
Processed 410000000 records
Processed 411000000 records
Processed 412000000 records
Processed 413000000 records
Processed 414000000 records
Processed 415000000 records
Processed 416000000 records
Processed 417000000 records
Processed 418000000 records
Processed 419000000 records
Processed 420000000 records
Processed 421000000 records
Processed 422000000 records
Processed 423000000 records
Processed 424000000 records
Processed 425000000 records
Processed 426000000 records
Processed 427000000 records
Processed 428000000 records
Processed 429000000 records
Processed 430000000 records
Processed 431000000 records
Processed 432000000 records
Processed 433000000 records
Processed 434000000 records
Processed 435000000 records
Processed 436000000 records
Processed 437000000 records
Processed 438000000 records
Processed 439000000 records
Processed 440000000 records
Processed 441000000 records
Processed 442000000 records
Processed 443000000 records
Processed 444000000 records
Processed 445000000 records
Processed 446000000 records
Processed 447000000 records
Processed 448000000 records
Processed 449000000 records
Processed 450000000 records
Processed 451000000 records
Processed 452000000 records
Processed 453000000 records
Processed 454000000 records
Processed 455000000 records
Processed 456000000 records
Processed 457000000 records
Processed 458000000 records
Processed 459000000 records
Processed 460000000 records
Processed 461000000 records
Processed 462000000 records
Processed 463000000 records
Processed 464000000 records
Processed 465000000 records
Processed 466000000 records
Processed 467000000 records
Processed 468000000 records
Processed 469000000 records
Processed 470000000 records
Processed 471000000 records
Processed 472000000 records
Processed 473000000 records
Processed 474000000 records
Processed 475000000 records
Processed 476000000 records
Processed 477000000 records
Processed 478000000 records
Processed 479000000 records
Processed 480000000 records
Processed 481000000 records
Processed 482000000 records
Processed 483000000 records
Processed 484000000 records
Processed 485000000 records
Processed 486000000 records
Processed 487000000 records
Processed 488000000 records
Processed 489000000 records
Processed 490000000 records
Processed 491000000 records
Processed 492000000 records
Processed 493000000 records
Processed 494000000 records
Processed 495000000 records
Processed 496000000 records
Processed 497000000 records
Processed 498000000 records
Processed 499000000 records
Processed 500000000 records
Processed 501000000 records
Processed 502000000 records
Processed 503000000 records
Processed 504000000 records
Processed 505000000 records
Processed 506000000 records
Processed 507000000 records
Processed 508000000 records
Processed 509000000 records
Processed 510000000 records
Processed 511000000 records
Processed 512000000 records
Processed 513000000 records
Processed 514000000 records
Processed 515000000 records
Processed 516000000 records
Processed 517000000 records
Processed 518000000 records
Processed 519000000 records
Processed 520000000 records
Processed 521000000 records
Processed 522000000 records
Processed 523000000 records
Processed 524000000 records
Processed 525000000 records
Processed 526000000 records
Processed 527000000 records
Processed 528000000 records
Processed 529000000 records
Processed 530000000 records
Processed 531000000 records
Processed 532000000 records
Processed 533000000 records
Processed 534000000 records
Processed 535000000 records
Processed 536000000 records
Processed 537000000 records
Processed 538000000 records
Processed 539000000 records
Processed 540000000 records
Processed 541000000 records
Processed 542000000 records
Processed 543000000 records
Processed 544000000 records
Processed 545000000 records
Processed 546000000 records
Processed 547000000 records
Processed 548000000 records
Processed 549000000 records
Processed 550000000 records
Processed 551000000 records
Processed 552000000 records
Processed 553000000 records
Processed 554000000 records
Processed 555000000 records
Processed 556000000 records
Processed 557000000 records
Processed 558000000 records
Processed 559000000 records
Processed 560000000 records
Processed 561000000 records
Processed 562000000 records
Processed 563000000 records
Processed 564000000 records
Processed 565000000 records
Processed 566000000 records
Processed 567000000 records
Processed 568000000 records
Processed 569000000 records
Processed 570000000 records
Processed 571000000 records
Processed 572000000 records
Processed 573000000 records
Processed 574000000 records
Processed 575000000 records
Processed 576000000 records
Processed 577000000 records
Processed 578000000 records
Processed 579000000 records
Processed 580000000 records
Processed 581000000 records
Processed 582000000 records
Processed 583000000 records
Processed 584000000 records
Processed 585000000 records
Processed 586000000 records
Processed 587000000 records
Processed 588000000 records
paired = 291648378
unpaired = 4862176
MERGED PAIRED END READS = 291648378
MATES PROCESSED = 588158932
TOTAL READS = 296510554
DISTINCT READS = 1.65553e+08
DISTINCT COUNTS = 752
MAX COUNT = 1003794
COUNTS OF 1 = 1.07755e+08
MAX TERMS = 100
OBSERVED COUNTS (1003795)
1 107754695
2 33121467
3 12079178
4 5170277
5 2559368
6 1430780
7 879302
8 579613
9 402405
10 291756
11 218088
12 167583
13 131827
14 104368
15 85245
16 70612
17 57835
18 48764
19 41649
20 35393
21 30604
22 26214
23 23173
24 20371
25 17954
26 15963
27 14249
28 12632
29 11250
30 10234
31 9424
32 8410
33 7647
34 7156
35 6383
36 5650
37 5280
38 4828
39 4478
40 4177
41 3987
42 3676
43 3310
44 3238
45 2941
46 2658
47 2532
48 2441
49 2230
50 2152
51 2019
52 1845
53 1731
54 1672
55 1632
56 1390
57 1424
58 1315
59 1235
60 1253
61 1160
62 1053
63 1036
64 966
65 895
66 871
67 824
68 748
69 746
70 730
71 683
72 639
73 680
74 677
75 604
76 521
77 532
78 522
79 546
80 466
81 462
82 435
83 406
84 409
85 361
86 385
87 358
88 348
89 338
90 337
91 328
92 320
93 295
94 296
95 279
96 258
97 278
98 259
99 245
100 217
101 237
102 217
103 218
104 194
105 186
106 190
107 203
108 199
109 171
110 173
111 144
112 165
113 172
114 156
115 145
116 145
117 160
118 157
119 133
120 125
121 130
122 110
123 124
124 102
125 122
126 116
127 95
128 112
129 96
130 90
131 117
132 101
133 93
134 76
135 80
136 90
137 79
138 77
139 98
140 76
141 79
142 68
143 69
144 65
145 70
146 58
147 68
148 69
149 52
150 60
151 70
152 71
153 59
154 60
155 51
156 65
157 47
158 61
159 60
160 54
161 62
162 59
163 54
164 55
165 50
166 44
167 36
168 41
169 50
170 40
171 47
172 32
173 43
174 48
175 50
176 36
177 34
178 39
179 26
180 28
181 34
182 28
183 36
184 24
185 23
186 33
187 37
188 30
189 27
190 33
191 29
192 28
193 27
194 29
195 37
196 24
197 22
198 22
199 28
200 28
201 23
202 15
203 29
204 20
205 18
206 27
207 12
208 22
209 28
210 25
211 24
212 20
213 22
214 26
215 21
216 20
217 12
218 22
219 16
220 18
221 19
222 7
223 17
224 22
225 15
226 17
227 17
228 21
229 20
230 16
231 16
232 13
233 15
234 10
235 15
236 13
237 14
238 15
239 17
240 16
241 15
242 17
243 13
244 13
245 8
246 15
247 13
248 9
249 11
250 8
251 19
252 16
253 9
254 9
255 14
256 16
257 12
258 6
259 12
260 16
261 16
262 8
263 11
264 9
265 15
266 7
267 9
268 12
269 18
270 11
271 10
272 11
273 8
274 5
275 7
276 8
277 9
278 11
279 7
280 12
281 11
282 9
283 12
284 6
285 10
286 4
287 7
288 7
289 5
290 7
291 8
292 9
293 8
294 7
295 9
296 8
297 7
298 6
299 5
300 8
301 6
302 6
303 8
304 8
305 3
306 8
307 5
308 6
309 5
310 5
311 7
312 6
313 6
314 4
315 9
316 6
317 5
318 6
319 3
320 8
321 2
322 6
323 5
324 4
325 3
326 5
327 12
328 6
329 4
330 1
331 6
332 4
333 7
334 5
335 4
336 2
338 7
339 4
340 1
341 5
342 6
343 3
344 2
345 5
346 5
347 3
348 1
349 2
350 5
351 3
352 3
353 5
354 5
355 6
356 5
357 5
358 3
359 4
360 4
361 4
362 2
363 5
364 6
365 9
366 6
367 5
368 3
369 4
370 3
371 3
372 5
373 4
374 3
375 8
376 2
377 4
378 7
379 2
380 2
381 3
382 1
383 2
384 4
385 2
386 2
387 1
388 4
390 5
391 1
392 2
394 4
395 2
396 5
397 2
398 3
399 7
400 5
401 4
402 1
403 4
404 1
405 1
406 6
407 3
408 6
409 4
410 3
411 3
412 1
414 2
415 1
416 1
417 5
418 3
419 3
420 2
421 1
422 2
423 2
424 2
426 1
428 4
429 2
430 3
431 6
432 1
433 2
434 2
435 1
437 3
438 3
439 3
441 1
442 1
443 1
444 2
445 1
446 3
448 2
449 1
450 1
452 1
453 2
454 1
457 3
458 1
459 1
460 3
461 3
462 4
463 4
464 2
465 2
466 2
467 1
468 1
469 1
470 1
471 2
472 3
473 2
474 3
476 3
477 1
478 2
479 2
480 1
481 2
483 1
484 1
485 1
486 1
487 2
488 1
489 2
491 1
493 1
494 2
496 1
497 1
498 2
499 1
500 1
502 2
503 3
505 1
506 1
507 3
508 1
509 2
514 2
515 1
517 3
520 1
521 1
522 3
523 1
525 1
526 1
527 1
531 2
533 1
536 3
537 3
538 3
539 2
540 2
541 1
542 1
544 1
545 1
547 2
550 1
552 1
553 2
554 2
558 1
560 1
561 1
562 3
563 2
565 1
569 1
570 1
571 2
573 1
574 1
576 2
579 1
580 1
581 1
582 3
584 1
587 1
589 1
591 3
592 2
593 1
596 1
597 1
600 1
602 2
603 1
606 1
612 1
616 1
617 1
619 1
621 1
622 2
623 4
625 1
626 1
627 2
629 2
630 1
633 2
634 2
635 3
636 2
637 2
638 2
642 1
644 1
647 1
649 1
653 1
656 1
657 2
661 1
666 2
673 1
678 2
681 1
684 1
694 1
696 1
701 1
706 4
709 1
710 1
711 1
716 1
720 1
721 1
723 1
725 1
726 1
727 1
729 1
730 1
731 1
732 1
733 1
737 1
738 1
740 1
747 1
752 1
763 2
773 1
774 1
777 1
778 1
782 1
783 1
784 1
785 3
787 1
792 1
801 2
805 2
806 1
807 1
812 2
815 1
825 1
829 1
832 1
833 1
855 1
868 2
871 1
885 1
887 1
893 1
898 1
904 1
905 1
906 1
915 1
923 1
932 1
938 1
939 1
943 1
947 1
950 1
954 1
958 1
976 2
983 1
987 1
995 1
1014 1
1015 2
1016 1
1022 1
1027 2
1028 1
1029 1
1034 1
1041 1
1075 1
1087 1
1088 1
1092 1
1100 2
1110 1
1115 1
1122 1
1124 1
1162 1
1166 1
1195 1
1201 1
1208 1
1225 1
1230 1
1287 1
1301 1
1304 1
1317 1
1336 1
1340 1
1345 1
1362 1
1371 1
1387 1
1394 1
1414 1
1430 1
1435 1
1461 1
1531 1
1559 1
1560 1
1575 1
1584 1
1600 1
1606 1
1689 2
1699 1
1756 1
1776 1
1788 1
1795 1
1808 1
1809 1
1820 1
1840 1
1845 1
1847 1
1849 1
1863 1
1899 1
1918 1
1920 1
1928 1
1957 2
1960 1
1996 1
1997 2
2008 1
2010 1
2018 1
2033 1
2064 1
2101 2
2121 1
2145 1
2163 1
2165 1
2199 1
2238 1
2253 1
2269 1
2275 1
2404 1
2453 1
2487 1
2563 1
2621 1
2794 1
2832 1
2947 1
2997 1
3010 1
3034 1
3087 1
3123 1
3131 1
3316 1
3543 1
3623 1
5032 1
8532 1
9884 1
11441 1
11507 1
35971 1
1003794 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
..._........_.__....._._...._.._.__..._.__...__.._._._.__._._._.._.._...
....._._.....__.........._._....._...._......_..........__....._.
[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]