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]