Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/cbcbe2c809898963decc5811902729/.command.sh Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/9f/ac5fa0604f5965c14eced2773443f2/659_bMa-T1-TRNA-1_B23MHV2LT4_1.Aligned.sortedByCoord.out.bam Downloading: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/a9/cbcbe2c809898963decc5811902729/.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 paired = 159279062 unpaired = 2680008 MERGED PAIRED END READS = 159279062 MATES PROCESSED = 321238132 TOTAL READS = 161959070 DISTINCT READS = 1.93631e+07 DISTINCT COUNTS = 1184 MAX COUNT = 504139 COUNTS OF 1 = 4.36618e+06 MAX TERMS = 100 OBSERVED COUNTS (504140) 1 4366181 2 1731694 3 1354719 4 1219116 5 1126465 6 1039481 7 953813 8 867778 9 783303 10 705179 11 626620 12 555721 13 489760 14 430234 15 376251 16 328034 17 285411 18 248148 19 214866 20 186022 21 161296 22 140409 23 121692 24 105792 25 92196 26 80437 27 70725 28 62458 29 54655 30 48656 31 43220 32 38851 33 34450 34 30639 35 27806 36 25054 37 22528 38 20644 39 18705 40 17180 41 15606 42 14505 43 13103 44 12239 45 11207 46 10378 47 9568 48 8900 49 8444 50 7889 51 7262 52 6716 53 6231 54 5809 55 5495 56 5068 57 4808 58 4348 59 4291 60 4001 61 3722 62 3574 63 3298 64 3078 65 2929 66 2809 67 2500 68 2373 69 2221 70 2196 71 2051 72 1849 73 1833 74 1767 75 1615 76 1548 77 1490 78 1431 79 1342 80 1230 81 1199 82 1130 83 1145 84 1113 85 1023 86 1006 87 928 88 871 89 825 90 822 91 818 92 789 93 712 94 760 95 756 96 630 97 624 98 623 99 595 100 574 101 565 102 584 103 565 104 539 105 528 106 491 107 470 108 496 109 449 110 445 111 418 112 451 113 398 114 375 115 366 116 355 117 350 118 353 119 374 120 331 121 311 122 306 123 297 124 298 125 279 126 293 127 278 128 260 129 295 130 290 131 261 132 241 133 256 134 228 135 232 136 245 137 241 138 227 139 210 140 196 141 221 142 182 143 202 144 183 145 201 146 183 147 173 148 164 149 183 150 163 151 159 152 154 153 187 154 145 155 151 156 144 157 157 158 140 159 132 160 140 161 122 162 133 163 113 164 142 165 137 166 107 167 127 168 108 169 114 170 115 171 110 172 110 173 115 174 81 175 89 176 97 177 111 178 87 179 86 180 83 181 107 182 103 183 71 184 91 185 97 186 81 187 82 188 87 189 94 190 103 191 81 192 84 193 98 194 77 195 68 196 67 197 81 198 88 199 76 200 71 201 58 202 89 203 81 204 70 205 67 206 70 207 59 208 61 209 68 210 68 211 61 212 77 213 51 214 63 215 56 216 53 217 63 218 51 219 63 220 53 221 47 222 47 223 49 224 54 225 48 226 59 227 48 228 51 229 58 230 59 231 50 232 53 233 31 234 51 235 49 236 54 237 56 238 39 239 37 240 35 241 56 242 56 243 49 244 39 245 42 246 37 247 38 248 28 249 28 250 37 251 42 252 36 253 36 254 31 255 34 256 31 257 38 258 39 259 34 260 42 261 29 262 25 263 41 264 26 265 37 266 24 267 32 268 25 269 28 270 36 271 25 272 32 273 31 274 32 275 32 276 24 277 39 278 32 279 31 280 28 281 26 282 31 283 22 284 26 285 26 286 25 287 30 288 35 289 25 290 22 291 25 292 22 293 23 294 27 295 18 296 24 297 28 298 17 299 28 300 23 301 12 302 21 303 23 304 20 305 18 306 28 307 16 308 23 309 23 310 23 311 19 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463 9 464 3 465 6 466 5 467 7 468 6 469 6 470 7 471 7 472 8 473 10 474 4 475 5 476 5 477 5 478 9 479 6 480 7 481 5 482 3 483 4 484 5 485 5 486 10 487 2 488 4 489 10 490 5 491 5 492 2 493 7 494 6 495 4 496 10 497 1 498 5 499 6 500 7 501 2 502 7 503 5 504 6 505 5 506 8 507 5 508 6 509 9 510 3 511 7 512 6 513 5 514 2 515 3 516 5 517 6 518 4 519 5 520 4 521 7 522 5 523 3 524 8 525 6 526 2 527 6 528 4 529 4 530 5 531 5 532 8 533 6 534 5 535 5 536 4 537 8 538 4 539 4 540 2 541 5 542 6 543 3 544 6 545 2 546 8 547 4 548 2 549 3 550 3 551 8 552 7 553 4 554 4 555 2 556 5 557 4 558 1 559 4 560 2 561 8 562 6 563 10 564 4 565 3 566 5 567 3 568 5 569 3 570 1 571 3 572 7 573 6 574 4 575 2 576 4 577 5 578 2 579 5 580 3 581 5 582 6 583 1 584 1 585 2 586 2 587 3 588 2 589 6 590 2 591 3 592 2 593 2 594 1 595 6 597 2 598 5 599 4 600 3 601 3 602 3 603 3 604 1 605 2 606 4 607 4 608 2 609 1 610 4 611 3 613 7 614 4 615 6 616 3 617 2 618 3 619 1 620 5 621 2 622 2 623 3 624 3 625 3 626 4 628 2 629 1 630 2 631 1 632 3 633 1 634 3 635 5 636 3 637 5 638 1 639 6 640 2 641 3 642 2 643 3 644 4 645 4 646 3 647 4 648 2 649 3 651 3 652 5 653 4 654 2 656 4 657 5 658 1 659 3 660 3 661 4 662 2 663 6 664 2 665 3 666 2 667 4 669 2 671 2 672 1 673 2 674 2 676 1 678 2 679 1 680 3 681 2 682 3 683 6 684 4 685 2 686 3 687 1 688 1 689 3 690 3 691 1 692 2 693 3 694 2 695 6 696 5 697 3 698 1 699 3 700 1 701 2 702 1 703 4 704 4 705 2 706 5 707 2 708 3 709 6 710 1 711 3 712 3 713 3 714 1 715 4 717 1 718 1 719 4 720 3 721 4 723 2 724 5 725 1 726 2 727 1 728 4 729 1 731 3 732 1 733 1 734 2 735 3 736 3 737 1 738 2 739 3 740 1 741 4 743 3 745 4 746 2 747 2 748 2 749 2 751 5 752 5 753 3 754 2 755 1 756 1 757 3 759 2 761 2 762 1 765 2 766 3 767 1 768 2 769 1 770 3 771 1 772 4 776 1 777 4 778 2 779 1 780 1 781 3 783 1 785 2 786 2 787 1 788 2 789 3 790 1 791 1 792 1 793 1 794 1 795 2 796 4 798 2 801 1 802 1 803 1 804 2 805 1 806 2 807 2 808 1 809 1 810 3 811 1 814 2 815 1 816 1 817 4 818 1 819 1 820 1 821 2 822 5 823 1 824 1 825 2 826 2 828 1 829 1 830 3 831 2 832 3 833 6 835 1 836 1 837 2 838 1 841 1 842 2 843 1 845 4 846 1 847 2 848 2 850 2 851 2 853 1 854 2 855 1 856 2 857 1 858 2 859 1 861 3 862 1 863 1 864 1 866 1 867 1 869 4 870 1 871 2 872 3 873 1 875 1 877 1 879 1 880 2 886 1 887 1 888 2 889 3 890 1 891 1 900 1 901 2 903 1 904 1 905 1 906 1 907 3 908 2 909 1 911 1 913 1 915 1 916 1 918 1 920 1 922 2 926 1 927 2 928 4 929 1 930 1 931 2 932 2 933 1 934 2 936 3 938 1 939 1 940 1 944 3 945 2 947 1 949 1 950 2 951 1 952 1 955 1 956 1 957 2 959 1 960 1 963 2 964 1 967 1 968 1 969 2 970 1 971 1 972 2 974 3 976 1 978 1 980 1 981 2 982 2 983 1 984 1 985 1 988 1 989 1 990 1 992 1 993 1 995 1 996 1 1002 3 1004 1 1009 1 1012 1 1016 1 1017 1 1018 2 1019 1 1020 1 1021 2 1022 1 1023 1 1024 1 1025 1 1027 1 1028 1 1030 3 1032 1 1034 1 1035 2 1036 2 1041 1 1046 2 1047 3 1050 1 1051 1 1054 2 1055 1 1059 2 1063 1 1065 1 1071 1 1072 1 1075 1 1076 1 1078 1 1079 1 1082 1 1086 1 1088 2 1089 1 1094 2 1108 1 1113 1 1114 2 1115 3 1116 2 1117 2 1118 2 1122 2 1124 1 1125 1 1126 1 1127 1 1129 1 1130 1 1132 1 1134 1 1137 1 1139 4 1144 1 1148 1 1149 1 1155 1 1162 1 1163 1 1164 3 1166 1 1170 1 1172 1 1173 2 1183 1 1191 1 1192 1 1196 2 1198 2 1199 1 1201 1 1204 1 1205 1 1206 1 1209 1 1214 1 1220 1 1226 1 1228 2 1232 1 1233 2 1235 1 1237 1 1241 1 1243 2 1247 3 1249 2 1250 1 1251 2 1253 1 1257 1 1258 1 1269 1 1270 1 1272 1 1276 1 1277 1 1279 1 1283 3 1285 1 1286 1 1288 1 1290 1 1295 1 1301 1 1305 1 1306 1 1310 1 1313 1 1314 1 1316 1 1317 1 1320 1 1327 2 1328 1 1333 1 1340 1 1342 1 1349 1 1351 1 1354 1 1356 1 1358 1 1360 1 1361 1 1362 1 1363 1 1367 1 1377 1 1384 1 1400 1 1402 1 1406 1 1409 1 1412 1 1416 1 1420 1 1422 1 1430 1 1431 1 1432 1 1438 1 1462 1 1463 1 1474 1 1476 1 1478 1 1479 1 1481 2 1484 2 1485 1 1486 1 1487 1 1488 1 1493 1 1494 1 1495 1 1505 2 1510 1 1517 2 1528 2 1532 2 1538 1 1544 1 1567 1 1573 1 1575 1 1577 1 1581 1 1584 1 1592 1 1598 1 1599 1 1601 1 1605 1 1609 1 1620 1 1625 1 1628 1 1641 1 1644 1 1646 1 1661 1 1662 1 1667 1 1668 1 1674 1 1682 1 1684 2 1685 1 1700 1 1704 1 1712 1 1714 1 1748 1 1765 1 1769 1 1843 1 1849 1 1850 1 1856 1 1865 1 1907 1 1913 1 1922 1 1941 1 1975 1 1983 1 1997 1 2007 1 2014 1 2029 1 2037 1 2043 1 2056 1 2058 1 2070 1 2086 1 2096 1 2131 1 2136 1 2137 1 2150 1 2153 1 2174 1 2177 1 2181 1 2209 1 2234 1 2294 1 2306 1 2330 1 2410 1 2439 1 2452 1 2461 1 2496 1 2506 1 2622 1 2634 1 2653 1 2672 1 2711 1 2725 1 2778 1 2806 1 2874 1 3055 1 3154 1 3192 1 3195 1 3467 1 3487 1 3516 1 3567 1 4099 1 4213 1 4550 1 4663 1 4703 1 4731 1 4956 1 6246 1 6552 1 7735 1 10214 1 12743 1 504139 1 [ESTIMATING YIELD CURVE] [BOOTSTRAPPING HISTOGRAM] ....................................................._.................. ............................. [COMPUTING CONFIDENCE INTERVALS] [WRITING OUTPUT]