Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/ec99de83693180e9ce2a981a625041/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/358042018d33530932b1c9d34313a0/tih_rna_sample_00594_B23MVV7LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c1/ec99de83693180e9ce2a981a625041/.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 Processed 589000000 records Processed 590000000 records paired = 292569239 unpaired = 5336606 MERGED PAIRED END READS = 292569239 MATES PROCESSED = 590475084 TOTAL READS = 297905845 DISTINCT READS = 1.4826e+08 DISTINCT COUNTS = 913 MAX COUNT = 1271078 COUNTS OF 1 = 8.62072e+07 MAX TERMS = 100 OBSERVED COUNTS (1271079) 1 86207206 2 32846464 3 13845124 4 6428665 5 3273440 6 1808995 7 1071738 8 676702 9 449698 10 312699 11 228068 12 169534 13 130884 14 103604 15 83215 16 68361 17 57160 18 47736 19 40741 20 35107 21 30115 22 26815 23 23514 24 20853 25 18644 26 16432 27 14743 28 13658 29 12335 30 11239 31 10059 32 9493 33 8631 34 7893 35 7292 36 6920 37 6295 38 5791 39 5399 40 5158 41 4802 42 4475 43 4210 44 3789 45 3650 46 3520 47 3256 48 3098 49 2913 50 2801 51 2533 52 2492 53 2379 54 2332 55 2027 56 2111 57 2006 58 1855 59 1755 60 1606 61 1644 62 1507 63 1439 64 1442 65 1309 66 1270 67 1294 68 1232 69 1237 70 1147 71 1054 72 1015 73 996 74 989 75 961 76 950 77 847 78 841 79 824 80 810 81 742 82 723 83 734 84 651 85 654 86 665 87 614 88 598 89 588 90 533 91 544 92 536 93 517 94 535 95 478 96 436 97 477 98 424 99 462 100 405 101 369 102 433 103 351 104 385 105 372 106 355 107 378 108 342 109 345 110 345 111 302 112 278 113 294 114 289 115 312 116 265 117 262 118 247 119 264 120 276 121 226 122 255 123 234 124 240 125 207 126 227 127 203 128 207 129 221 130 203 131 190 132 188 133 202 134 166 135 183 136 175 137 176 138 165 139 176 140 152 141 160 142 181 143 153 144 141 145 146 146 162 147 150 148 126 149 148 150 154 151 124 152 125 153 120 154 134 155 127 156 116 157 138 158 123 159 112 160 115 161 100 162 106 163 115 164 106 165 107 166 126 167 119 168 107 169 88 170 93 171 85 172 108 173 82 174 76 175 96 176 70 177 88 178 76 179 86 180 88 181 92 182 71 183 75 184 60 185 80 186 64 187 63 188 66 189 76 190 55 191 68 192 73 193 62 194 74 195 71 196 64 197 56 198 61 199 62 200 50 201 73 202 61 203 62 204 54 205 60 206 57 207 47 208 41 209 49 210 54 211 49 212 60 213 43 214 50 215 42 216 53 217 35 218 48 219 37 220 47 221 50 222 33 223 39 224 35 225 46 226 45 227 47 228 45 229 47 230 43 231 42 232 48 233 40 234 47 235 31 236 32 237 39 238 30 239 30 240 38 241 50 242 37 243 34 244 39 245 31 246 25 247 33 248 33 249 26 250 34 251 24 252 27 253 31 254 43 255 27 256 30 257 30 258 26 259 36 260 23 261 21 262 23 263 18 264 30 265 31 266 24 267 17 268 20 269 27 270 27 271 24 272 28 273 19 274 23 275 29 276 30 277 15 278 30 279 30 280 27 281 15 282 19 283 27 284 20 285 22 286 15 287 15 288 19 289 21 290 14 291 13 292 13 293 11 294 20 295 16 296 13 297 32 298 15 299 14 300 9 301 12 302 16 303 21 304 17 305 15 306 8 307 12 308 16 309 17 310 14 311 15 312 9 313 9 314 13 315 9 316 12 317 11 318 13 319 19 320 13 321 16 322 11 323 11 324 14 325 12 326 15 327 12 328 10 329 11 330 13 331 10 332 14 333 10 334 12 335 13 336 15 337 14 338 10 339 14 340 17 341 10 342 12 343 7 344 7 345 15 346 5 347 11 348 11 349 9 350 10 351 13 352 8 353 8 354 12 355 10 356 6 357 7 358 9 359 7 360 10 361 7 362 11 363 9 364 9 365 9 366 11 367 7 368 15 369 11 370 10 371 11 372 6 373 3 374 5 375 7 376 13 377 11 378 8 379 6 380 9 381 13 382 9 383 9 384 9 385 7 386 11 387 6 388 5 389 9 390 3 391 8 392 10 393 10 394 5 395 7 396 8 397 7 398 8 399 5 400 2 401 8 402 7 403 5 404 8 405 4 406 4 407 5 408 12 409 10 410 5 411 2 412 6 413 5 414 6 415 6 416 6 417 7 418 7 419 8 420 12 421 8 422 6 423 8 424 9 426 7 427 5 428 3 429 5 430 2 431 8 432 8 433 6 434 9 435 5 436 3 437 6 438 1 439 6 440 4 441 5 442 5 443 5 444 6 445 6 446 8 447 5 448 5 449 2 450 3 451 4 452 3 453 7 454 5 455 4 456 2 457 6 458 6 459 4 460 4 461 10 462 3 463 3 464 7 465 1 466 6 467 3 468 5 469 3 470 5 471 4 472 6 473 4 474 1 475 5 476 2 477 8 478 4 479 4 480 5 481 2 482 3 483 2 484 3 485 4 486 3 487 5 488 2 489 3 490 3 491 3 492 4 493 4 494 3 495 4 496 2 497 4 498 5 499 3 500 1 501 1 502 3 503 6 504 5 505 1 506 6 507 2 508 3 509 6 510 4 511 3 512 3 513 11 514 2 515 1 516 3 517 3 518 1 520 1 521 4 522 4 524 4 525 2 526 5 528 4 529 3 530 1 531 3 532 2 533 2 534 2 535 1 537 2 538 2 539 4 540 4 542 4 543 3 544 4 545 6 546 1 547 1 548 1 550 1 551 5 552 3 553 2 554 4 555 2 556 3 557 1 558 2 560 1 561 3 562 2 563 2 564 1 565 3 566 3 567 2 568 4 569 1 570 2 572 3 573 1 574 4 575 1 577 1 578 2 579 6 580 1 582 4 583 3 584 2 587 1 589 2 590 1 591 3 592 1 596 3 597 3 598 2 600 1 602 1 603 1 604 1 607 1 609 3 610 4 611 1 612 1 613 1 614 1 616 1 618 1 619 3 620 1 621 4 623 3 624 3 625 1 626 1 627 2 628 2 629 2 630 2 631 1 633 4 634 1 635 1 637 3 638 3 640 1 641 1 642 2 643 2 644 1 647 1 648 2 649 1 650 3 651 1 652 1 653 2 655 1 657 1 658 2 659 2 661 2 664 1 665 1 666 2 668 2 670 2 671 2 672 2 674 1 675 2 676 2 677 1 678 1 679 1 680 2 683 1 686 1 687 1 688 1 689 1 690 1 691 2 692 2 697 1 698 2 699 1 701 1 702 2 703 1 704 1 706 2 707 1 710 2 711 1 714 1 716 2 717 1 718 1 720 1 726 2 727 1 730 1 732 1 737 1 738 1 740 1 741 1 742 1 743 1 744 1 746 2 750 1 751 1 752 3 754 2 755 1 757 3 758 1 761 1 765 1 768 1 770 1 772 1 773 1 774 1 776 1 778 1 779 1 787 1 791 1 792 1 793 1 794 1 795 1 796 1 797 1 801 1 805 1 809 1 812 1 814 1 815 1 817 1 819 2 822 1 826 2 828 2 829 3 832 2 835 1 837 2 840 5 841 1 844 1 848 1 850 1 853 1 855 1 856 1 858 2 862 1 864 1 865 1 866 2 871 1 873 1 874 1 876 1 879 1 881 1 882 2 885 2 886 1 888 1 898 1 903 1 905 1 906 1 909 1 910 1 912 1 918 1 922 2 923 1 930 1 932 1 933 1 935 1 936 1 940 1 942 2 955 1 956 2 965 1 967 1 972 1 983 1 984 1 985 1 989 1 996 1 998 1 999 1 1002 1 1003 1 1008 1 1012 1 1014 1 1016 1 1017 1 1036 1 1043 1 1061 1 1065 1 1067 2 1068 1 1069 1 1072 1 1075 1 1083 3 1090 1 1099 1 1100 1 1102 1 1116 1 1117 1 1122 1 1133 1 1163 2 1169 1 1171 1 1177 1 1181 1 1202 1 1221 1 1227 1 1238 1 1240 1 1249 1 1264 1 1279 1 1280 1 1291 1 1294 1 1301 1 1321 1 1344 1 1370 1 1391 1 1395 1 1397 1 1404 1 1430 1 1437 1 1441 1 1455 1 1547 1 1604 1 1654 1 1711 1 1715 1 1743 1 1748 1 1750 1 1787 1 1797 1 1823 1 1834 1 1846 1 1849 1 1858 1 1863 2 1869 1 1877 1 1885 1 1891 1 1899 1 1907 1 1910 1 1916 1 1925 1 1929 1 1943 1 1950 1 1967 1 1977 1 1982 1 1997 2 2001 1 2040 1 2064 1 2118 1 2124 1 2154 1 2193 1 2206 1 2225 2 2235 1 2243 1 2264 2 2284 1 2286 1 2292 1 2295 1 2300 1 2305 1 2318 1 2344 1 2350 1 2354 1 2362 1 2408 1 2454 1 2458 1 2462 1 2602 1 2651 1 2698 1 2702 1 2718 1 2738 1 2748 1 2755 1 2769 1 2801 1 2881 1 2917 1 3103 1 3123 1 3224 1 3295 1 3335 1 3543 1 3608 1 3833 1 3967 1 4265 1 4656 1 5174 1 5473 1 7305 1 7783 1 10652 1 12691 1 28963 1 1271078 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] .........._....._......._._........_........_.._._.___.._....._......... __......._.........._...._...____........__......... [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]