Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/d6cae2ee1c6f340efb241b168d9f0d/.command.sh
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/3e8a82e76bbc12a902ec65f52defc1/BreastNP_FFPE_L04_RNA_01_B23LG7FLT4_1.Aligned.sortedByCoord.out.bam
Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/f2/d6cae2ee1c6f340efb241b168d9f0d/.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
paired = 32460396
unpaired = 731573
MERGED PAIRED END READS = 32460396
MATES PROCESSED = 65652365
TOTAL READS = 33191969
DISTINCT READS = 3.19467e+06
DISTINCT COUNTS = 604
MAX COUNT = 101849
COUNTS OF 1 = 1.20422e+06
MAX TERMS = 100
OBSERVED COUNTS (101850)
1 1204223
2 380801
3 157013
4 94890
5 75660
6 68571
7 64338
8 61515
9 58964
10 56816
11 54602
12 52311
13 50389
14 47476
15 45258
16 42921
17 40977
18 38589
19 36287
20 34451
21 32562
22 30486
23 28521
24 26957
25 25077
26 23437
27 21783
28 20656
29 19463
30 17673
31 16873
32 15691
33 14581
34 13722
35 12743
36 11793
37 10896
38 10259
39 9683
40 9107
41 8631
42 7852
43 7245
44 6853
45 6573
46 6073
47 5755
48 5427
49 5034
50 4583
51 4560
52 4139
53 3901
54 3606
55 3460
56 3279
57 3092
58 2891
59 2748
60 2632
61 2494
62 2284
63 2151
64 2100
65 1938
66 1882
67 1762
68 1738
69 1614
70 1483
71 1413
72 1388
73 1324
74 1237
75 1137
76 1102
77 1059
78 1038
79 1047
80 910
81 946
82 896
83 788
84 787
85 814
86 784
87 709
88 699
89 633
90 559
91 565
92 553
93 597
94 534
95 524
96 460
97 490
98 463
99 433
100 446
101 400
102 402
103 371
104 366
105 359
106 367
107 343
108 295
109 348
110 295
111 336
112 299
113 293
114 274
115 267
116 269
117 248
118 245
119 280
120 193
121 215
122 203
123 225
124 185
125 177
126 197
127 202
128 179
129 176
130 177
131 163
132 158
133 168
134 171
135 152
136 134
137 150
138 141
139 121
140 123
141 114
142 106
143 124
144 116
145 111
146 117
147 104
148 95
149 108
150 108
151 79
152 76
153 92
154 85
155 80
156 79
157 77
158 65
159 92
160 53
161 60
162 59
163 54
164 70
165 44
166 62
167 55
168 48
169 43
170 54
171 62
172 51
173 45
174 45
175 45
176 45
177 37
178 34
179 38
180 30
181 34
182 33
183 29
184 32
185 27
186 43
187 28
188 27
189 32
190 23
191 26
192 21
193 27
194 23
195 23
196 30
197 18
198 21
199 16
200 11
201 20
202 20
203 16
204 21
205 30
206 12
207 20
208 11
209 18
210 20
211 14
212 19
213 15
214 19
215 25
216 12
217 17
218 12
219 10
220 9
221 13
222 13
223 9
224 20
225 15
226 12
227 10
228 15
229 5
230 9
231 9
232 14
233 16
234 6
235 11
236 10
237 10
238 5
239 17
240 11
241 16
242 7
243 9
244 8
245 9
246 11
247 15
248 14
249 8
250 7
251 5
252 9
253 13
254 10
255 9
256 9
257 5
258 5
259 7
260 6
261 3
262 4
263 3
264 3
265 6
266 6
267 3
268 6
269 2
270 5
271 6
272 7
273 8
274 9
275 13
276 5
277 8
278 7
279 7
280 5
281 8
282 1
283 6
284 3
285 2
286 5
287 3
288 4
289 5
290 5
291 7
292 10
293 7
294 8
295 2
296 7
297 4
298 6
299 4
300 3
301 1
302 4
303 6
304 5
305 6
306 5
307 3
308 1
309 4
310 2
311 4
312 6
313 6
314 6
315 4
316 2
317 1
318 4
319 4
320 1
321 3
322 6
323 2
324 3
325 3
327 2
328 4
329 6
330 7
331 4
332 1
333 5
334 3
335 4
336 2
337 3
338 1
339 2
340 3
341 3
342 5
343 1
344 2
345 1
346 3
347 1
348 1
349 4
350 2
351 2
352 1
353 5
356 3
357 1
358 1
359 1
360 2
361 3
362 1
363 1
364 1
365 2
366 2
367 1
368 2
369 4
370 4
371 2
372 2
374 1
375 2
377 3
378 1
380 2
381 2
382 1
383 2
384 1
386 2
387 3
388 1
389 4
390 2
391 3
392 1
393 2
394 1
395 2
397 2
398 1
400 1
401 2
402 3
403 2
405 1
406 1
409 1
410 1
411 1
412 2
413 2
414 1
416 3
417 2
419 1
420 4
421 1
423 1
424 2
425 2
426 2
427 2
430 6
431 2
432 2
433 1
435 2
438 3
439 1
440 2
441 2
442 1
443 1
444 2
445 1
447 1
449 1
452 2
453 1
454 1
455 1
456 2
458 1
460 1
461 1
462 1
464 2
465 1
467 2
470 1
471 2
472 1
473 2
474 1
475 1
477 2
479 2
480 2
481 1
482 2
484 1
487 3
488 2
490 1
491 1
494 3
495 1
496 2
500 2
503 1
505 2
506 2
507 1
510 2
511 2
512 1
517 1
522 2
523 2
524 1
526 1
529 1
533 1
535 1
540 1
542 1
545 2
546 2
547 2
550 1
553 2
554 1
556 1
567 1
572 2
573 1
575 1
580 1
584 2
594 1
595 2
596 1
597 1
599 1
603 1
604 1
607 1
608 1
610 2
611 1
616 2
617 2
619 1
621 1
626 1
627 1
628 2
629 1
630 1
633 1
637 1
643 1
645 1
651 1
658 1
659 1
661 1
662 1
665 1
675 2
676 1
680 1
684 1
694 1
695 1
698 1
701 1
702 1
718 1
723 1
731 1
733 1
736 1
738 1
752 1
772 1
773 1
774 1
781 1
784 1
788 1
789 1
792 1
796 1
805 1
826 1
829 1
849 1
861 1
866 1
874 1
882 1
894 1
901 1
909 1
913 1
916 1
923 1
925 1
928 1
930 1
931 1
1008 1
1018 1
1021 1
1039 1
1041 1
1048 1
1055 1
1079 1
1110 1
1139 1
1144 1
1153 1
1154 1
1161 1
1171 1
1172 1
1178 1
1226 1
1243 1
1258 1
1286 1
1298 1
1301 1
1314 1
1376 1
1393 1
1492 1
1557 1
1600 1
1689 1
2092 1
2282 1
2440 1
2720 1
2845 1
2870 1
2972 1
3347 1
3412 1
4251 1
5669 1
101849 1
[ESTIMATING YIELD CURVE]
[BOOTSTRAPPING HISTOGRAM]
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[COMPUTING CONFIDENCE INTERVALS]
[WRITING OUTPUT]