********************************************************* * GCTB 2.5.6 beta * * Genome-wide Complex Trait Bayesian analysis * * For inquiries, contact: Jian Zeng * * Last updated: 24 May, 2026 * * MIT License * ********************************************************* Options: --ldm-eigen ldm_eigen --gwas-summary gwas.ma --impute-summary --thread 4 --out gwas Using 4 threads. Analysis started: Sat Jun 6 20:00:57 2026 Reading LD matrix eigen-decomposition data... Reading LDM info from file [ldm_eigen/ldm.info]. 590 LD Blocks to be included from [ldm_eigen/ldm.info]. Reading LDM SNP info from file [ldm_eigen/snp.info]. 272826 SNPs to be included from [ldm_eigen/snp.info]. Reading GWAS summary data from [gwas.ma]. Removed 7839 SNPs with per-SNP sample size beyond 3 SD around the median value. 264987 matched SNPs in the GWAS summary data (in total 273604 SNPs). Reading per-block eigen binaries under [ldm_eigen] (590 blocks, serial) ... Block TotalSNPs Anchors ToImpute PctImpute 1 198 181 17 0.086 2 319 312 7 0.022 3 361 352 9 0.025 4 201 193 8 0.040 5 281 272 9 0.032 6 436 430 6 0.014 7 229 221 8 0.035 8 504 500 4 0.008 9 522 515 7 0.013 10 426 421 5 0.012 11 247 243 4 0.016 12 530 522 8 0.015 13 505 491 14 0.028 14 346 338 8 0.023 15 341 338 3 0.009 16 443 435 8 0.018 17 384 379 5 0.013 18 459 452 7 0.015 19 670 643 27 0.040 20 431 407 24 0.056 21 442 429 13 0.029 22 332 326 6 0.018 23 547 536 11 0.020 24 473 456 17 0.036 25 610 588 22 0.036 26 370 364 6 0.016 27 516 501 15 0.029 28 710 698 12 0.017 29 514 506 8 0.016 30 662 648 14 0.021 31 463 452 11 0.024 32 672 662 10 0.015 33 514 509 5 0.010 34 467 450 17 0.036 35 561 537 24 0.043 36 575 559 16 0.028 37 288 284 4 0.014 38 682 669 13 0.019 39 393 381 12 0.031 40 492 480 12 0.024 41 450 448 2 0.004 42 585 575 10 0.017 43 348 341 7 0.020 44 281 276 5 0.018 45 213 206 7 0.033 46 440 431 9 0.020 47 121 118 3 0.025 48 418 403 15 0.036 49 105 102 3 0.029 50 461 449 12 0.026 51 354 343 11 0.031 52 415 408 7 0.017 53 289 284 5 0.017 54 391 381 10 0.026 55 366 351 15 0.041 56 351 344 7 0.020 57 461 453 8 0.017 58 318 314 4 0.013 59 504 489 15 0.030 60 477 464 13 0.027 61 447 429 18 0.040 62 433 426 7 0.016 63 702 671 31 0.044 64 635 611 24 0.038 65 759 746 13 0.017 66 406 397 9 0.022 67 558 550 8 0.014 68 547 531 16 0.029 69 535 523 12 0.022 70 788 774 14 0.018 71 348 343 5 0.014 72 573 561 12 0.021 73 546 532 14 0.026 74 540 528 12 0.022 75 457 444 13 0.028 76 550 539 11 0.020 77 475 461 14 0.029 78 559 545 14 0.025 79 511 491 20 0.039 80 627 608 19 0.030 81 469 456 13 0.028 82 417 410 7 0.017 83 612 598 14 0.023 84 736 711 25 0.034 85 363 350 13 0.036 86 629 617 12 0.019 87 407 399 8 0.020 88 536 506 30 0.056 89 344 336 8 0.023 90 391 381 10 0.026 91 557 539 18 0.032 92 438 423 15 0.034 93 464 455 9 0.019 94 235 232 3 0.013 95 564 533 31 0.055 96 522 501 21 0.040 97 475 463 12 0.025 98 406 396 10 0.025 99 348 343 5 0.014 100 412 404 8 0.019 101 412 403 9 0.022 102 556 528 28 0.050 103 435 427 8 0.018 104 365 359 6 0.016 105 459 442 17 0.037 106 509 498 11 0.022 107 638 625 13 0.020 108 486 476 10 0.021 109 494 480 14 0.028 110 543 534 9 0.017 111 545 538 7 0.013 112 516 509 7 0.014 113 509 492 17 0.033 114 1009 957 52 0.052 115 690 669 21 0.030 116 507 495 12 0.024 117 389 380 9 0.023 118 557 542 15 0.027 119 431 424 7 0.016 120 473 465 8 0.017 121 383 373 10 0.026 122 721 707 14 0.019 123 579 551 28 0.048 124 481 461 20 0.042 125 559 546 13 0.023 126 690 657 33 0.048 127 351 342 9 0.026 128 344 336 8 0.023 129 469 453 16 0.034 130 343 334 9 0.026 131 317 308 9 0.028 132 263 259 4 0.015 133 477 467 10 0.021 134 282 271 11 0.039 135 344 328 16 0.047 136 329 310 19 0.058 137 318 315 3 0.009 138 234 223 11 0.047 139 634 615 19 0.030 140 380 372 8 0.021 141 676 659 17 0.025 142 356 344 12 0.034 143 436 412 24 0.055 144 447 424 23 0.051 145 596 580 16 0.027 146 763 734 29 0.038 147 358 347 11 0.031 148 564 527 37 0.066 149 506 493 13 0.026 150 385 381 4 0.010 151 479 467 12 0.025 152 504 492 12 0.024 153 471 448 23 0.049 154 597 578 19 0.032 155 618 596 22 0.036 156 407 396 11 0.027 157 708 682 26 0.037 158 539 519 20 0.037 159 578 538 40 0.069 160 503 482 21 0.042 161 516 500 16 0.031 162 319 310 9 0.028 163 386 364 22 0.057 164 631 595 36 0.057 165 348 330 18 0.052 166 598 574 24 0.040 167 249 240 9 0.036 168 351 335 16 0.046 169 402 385 17 0.042 170 255 246 9 0.035 171 512 488 24 0.047 172 412 386 26 0.063 173 355 345 10 0.028 174 475 461 14 0.029 175 366 354 12 0.033 176 391 382 9 0.023 177 373 360 13 0.035 178 371 346 25 0.067 179 677 650 27 0.040 180 309 307 2 0.006 181 519 507 12 0.023 182 839 811 28 0.033 183 397 390 7 0.018 184 846 828 18 0.021 185 396 394 2 0.005 186 424 415 9 0.021 187 498 481 17 0.034 188 430 409 21 0.049 189 646 623 23 0.036 190 684 652 32 0.047 191 589 560 29 0.049 192 574 558 16 0.028 193 479 461 18 0.038 194 591 567 24 0.041 195 741 724 17 0.023 196 673 667 6 0.009 197 502 490 12 0.024 198 478 467 11 0.023 199 607 601 6 0.010 200 379 371 8 0.021 201 422 408 14 0.033 202 370 366 4 0.011 203 395 389 6 0.015 204 371 365 6 0.016 205 257 252 5 0.019 206 222 210 12 0.054 207 225 216 9 0.040 208 310 306 4 0.013 209 318 310 8 0.025 210 316 310 6 0.019 211 448 426 22 0.049 212 351 345 6 0.017 213 517 505 12 0.023 214 342 337 5 0.015 215 447 431 16 0.036 216 1386 1344 42 0.030 217 472 461 11 0.023 218 595 586 9 0.015 219 357 347 10 0.028 220 662 640 22 0.033 221 782 746 36 0.046 222 841 802 39 0.046 223 644 624 20 0.031 224 731 707 24 0.033 225 566 549 17 0.030 226 663 628 35 0.053 227 481 457 24 0.050 228 482 474 8 0.017 229 652 630 22 0.034 230 820 788 32 0.039 231 726 708 18 0.025 232 354 344 10 0.028 233 290 279 11 0.038 234 626 607 19 0.030 235 498 489 9 0.018 236 441 431 10 0.023 237 524 506 18 0.034 238 611 597 14 0.023 239 478 467 11 0.023 240 671 651 20 0.030 241 418 407 11 0.026 242 270 260 10 0.037 243 236 226 10 0.042 244 496 468 28 0.056 245 343 326 17 0.050 246 535 521 14 0.026 247 437 418 19 0.043 248 740 722 18 0.024 249 407 400 7 0.017 250 542 526 16 0.030 251 483 474 9 0.019 252 428 419 9 0.021 253 488 472 16 0.033 254 538 517 21 0.039 255 549 531 18 0.033 256 395 383 12 0.030 257 398 385 13 0.033 258 425 399 26 0.061 259 712 689 23 0.032 260 423 414 9 0.021 261 600 583 17 0.028 262 388 379 9 0.023 263 445 420 25 0.056 264 595 575 20 0.034 265 840 818 22 0.026 266 243 238 5 0.021 267 580 563 17 0.029 268 337 329 8 0.024 269 492 477 15 0.030 270 268 258 10 0.037 271 290 278 12 0.041 272 307 298 9 0.029 273 250 239 11 0.044 274 358 344 14 0.039 275 515 496 19 0.037 276 482 467 15 0.031 277 742 725 17 0.023 278 600 577 23 0.038 279 368 359 9 0.024 280 465 459 6 0.013 281 469 456 13 0.028 282 487 475 12 0.025 283 543 530 13 0.024 284 707 673 34 0.048 285 558 538 20 0.036 286 625 608 17 0.027 287 576 558 18 0.031 288 390 384 6 0.015 289 834 809 25 0.030 290 725 698 27 0.037 291 577 557 20 0.035 292 562 549 13 0.023 293 395 389 6 0.015 294 866 829 37 0.043 295 729 704 25 0.034 296 655 640 15 0.023 297 495 484 11 0.022 298 659 645 14 0.021 299 523 510 13 0.025 300 641 621 20 0.031 301 609 565 44 0.072 302 377 368 9 0.024 303 281 276 5 0.018 304 353 342 11 0.031 305 570 564 6 0.011 306 463 440 23 0.050 307 616 582 34 0.055 308 590 575 15 0.025 309 531 510 21 0.040 310 351 337 14 0.040 311 480 463 17 0.035 312 543 520 23 0.042 313 520 506 14 0.027 314 733 718 15 0.020 315 446 440 6 0.013 316 447 439 8 0.018 317 499 491 8 0.016 318 408 398 10 0.025 319 459 450 9 0.020 320 720 703 17 0.024 321 707 693 14 0.020 322 469 459 10 0.021 323 609 595 14 0.023 324 456 450 6 0.013 325 574 558 16 0.028 326 411 402 9 0.022 327 673 650 23 0.034 328 524 505 19 0.036 329 271 255 16 0.059 330 425 412 13 0.031 331 426 415 11 0.026 332 348 343 5 0.014 333 408 397 11 0.027 334 335 330 5 0.015 335 398 396 2 0.005 336 407 396 11 0.027 337 436 422 14 0.032 338 407 402 5 0.012 339 445 433 12 0.027 340 470 458 12 0.026 341 592 570 22 0.037 342 640 621 19 0.030 343 625 603 22 0.035 344 792 769 23 0.029 345 542 533 9 0.017 346 595 585 10 0.017 347 304 293 11 0.036 348 689 681 8 0.012 349 497 486 11 0.022 350 466 460 6 0.013 351 677 669 8 0.012 352 622 615 7 0.011 353 389 382 7 0.018 354 300 297 3 0.010 355 412 406 6 0.015 356 388 382 6 0.015 357 261 256 5 0.019 358 238 232 6 0.025 359 328 301 27 0.082 360 348 308 40 0.115 361 437 424 13 0.030 362 331 328 3 0.009 363 550 537 13 0.024 364 470 463 7 0.015 365 439 433 6 0.014 366 319 310 9 0.028 367 405 386 19 0.047 368 397 388 9 0.023 369 386 381 5 0.013 370 653 636 17 0.026 371 921 896 25 0.027 372 477 464 13 0.027 373 375 370 5 0.013 374 632 618 14 0.022 375 643 628 15 0.023 376 528 501 27 0.051 377 426 408 18 0.042 378 531 513 18 0.034 379 618 592 26 0.042 380 355 344 11 0.031 381 469 462 7 0.015 382 470 463 7 0.015 383 344 342 2 0.006 384 471 461 10 0.021 385 385 381 4 0.010 386 425 421 4 0.009 387 194 187 7 0.036 388 309 304 5 0.016 389 272 266 6 0.022 390 305 293 12 0.039 391 238 232 6 0.025 392 437 419 18 0.041 393 405 399 6 0.015 394 509 482 27 0.053 395 534 515 19 0.036 396 538 523 15 0.028 397 925 898 27 0.029 398 620 602 18 0.029 399 468 459 9 0.019 400 335 328 7 0.021 401 678 661 17 0.025 402 564 547 17 0.030 403 619 595 24 0.039 404 344 334 10 0.029 405 658 638 20 0.030 406 569 559 10 0.018 407 357 348 9 0.025 408 448 439 9 0.020 409 417 409 8 0.019 410 416 408 8 0.019 411 564 558 6 0.011 412 252 249 3 0.012 413 259 251 8 0.031 414 597 590 7 0.012 415 428 424 4 0.009 416 165 163 2 0.012 417 147 134 13 0.088 418 419 407 12 0.029 419 225 217 8 0.036 420 243 239 4 0.016 421 430 424 6 0.014 422 357 353 4 0.011 423 410 399 11 0.027 424 531 514 17 0.032 425 620 610 10 0.016 426 481 471 10 0.021 427 759 729 30 0.040 428 959 904 55 0.057 429 418 408 10 0.024 430 393 376 17 0.043 431 484 454 30 0.062 432 952 897 55 0.058 433 454 443 11 0.024 434 407 402 5 0.012 435 494 477 17 0.034 436 314 306 8 0.025 437 296 281 15 0.051 438 255 254 1 0.004 439 452 440 12 0.027 440 324 312 12 0.037 441 432 424 8 0.019 442 337 325 12 0.036 443 376 363 13 0.035 444 361 354 7 0.019 445 457 437 20 0.044 446 699 665 34 0.049 447 522 508 14 0.027 448 407 401 6 0.015 449 579 566 13 0.022 450 641 632 9 0.014 451 525 515 10 0.019 452 437 429 8 0.018 453 599 580 19 0.032 454 579 568 11 0.019 455 399 387 12 0.030 456 269 264 5 0.019 457 247 244 3 0.012 458 321 312 9 0.028 459 244 220 24 0.098 460 571 555 16 0.028 461 233 223 10 0.043 462 479 475 4 0.008 463 433 420 13 0.030 464 286 280 6 0.021 465 658 641 17 0.026 466 501 488 13 0.026 467 602 587 15 0.025 468 324 317 7 0.022 469 505 498 7 0.014 470 239 233 6 0.025 471 734 723 11 0.015 472 566 545 21 0.037 473 401 394 7 0.017 474 497 484 13 0.026 475 149 148 1 0.007 476 370 360 10 0.027 477 249 241 8 0.032 478 253 209 44 0.174 479 330 318 12 0.036 480 309 303 6 0.019 481 348 343 5 0.014 482 339 329 10 0.029 483 296 292 4 0.014 484 316 311 5 0.016 485 274 272 2 0.007 486 411 402 9 0.022 487 747 725 22 0.029 488 472 455 17 0.036 489 345 338 7 0.020 490 398 388 10 0.025 491 513 508 5 0.010 492 532 520 12 0.023 493 580 572 8 0.014 494 427 415 12 0.028 495 359 355 4 0.011 496 256 247 9 0.035 497 148 146 2 0.014 498 142 129 13 0.092 499 88 79 9 0.102 500 146 142 4 0.027 501 315 307 8 0.025 502 241 235 6 0.025 503 197 193 4 0.020 504 334 329 5 0.015 505 319 311 8 0.025 506 205 202 3 0.015 507 287 281 6 0.021 508 569 554 15 0.026 509 533 524 9 0.017 510 273 266 7 0.026 511 394 386 8 0.020 512 624 610 14 0.022 513 569 556 13 0.023 514 354 342 12 0.034 515 700 686 14 0.020 516 563 551 12 0.021 517 422 412 10 0.024 518 204 189 15 0.074 519 230 220 10 0.043 520 261 251 10 0.038 521 255 245 10 0.039 522 181 178 3 0.017 523 564 553 11 0.020 524 294 284 10 0.034 525 816 800 16 0.020 526 627 600 27 0.043 527 696 684 12 0.017 528 779 763 16 0.021 529 433 423 10 0.023 530 587 573 14 0.024 531 780 770 10 0.013 532 479 471 8 0.017 533 323 309 14 0.043 534 573 543 30 0.052 535 603 586 17 0.028 536 444 436 8 0.018 537 343 323 20 0.058 538 194 166 28 0.144 539 263 246 17 0.065 540 250 239 11 0.044 541 183 178 5 0.027 542 448 439 9 0.020 543 206 202 4 0.019 544 280 273 7 0.025 545 277 265 12 0.043 546 4 4 0 0.000 547 337 332 5 0.015 548 522 505 17 0.033 549 302 295 7 0.023 550 192 183 9 0.047 551 219 213 6 0.027 552 295 287 8 0.027 553 83 81 2 0.024 554 375 367 8 0.021 555 425 418 7 0.016 556 430 419 11 0.026 557 230 224 6 0.026 558 347 340 7 0.020 559 225 222 3 0.013 560 664 648 16 0.024 561 445 435 10 0.022 562 340 331 9 0.026 563 628 611 17 0.027 564 517 507 10 0.019 565 238 234 4 0.017 566 456 447 9 0.020 567 634 623 11 0.017 568 458 449 9 0.020 569 231 223 8 0.035 570 487 440 47 0.097 571 533 508 25 0.047 572 448 424 24 0.054 573 322 312 10 0.031 574 569 554 15 0.026 575 509 491 18 0.035 576 440 429 11 0.025 577 487 480 7 0.014 578 474 465 9 0.019 579 592 586 6 0.010 580 482 453 29 0.060 581 297 292 5 0.017 582 379 367 12 0.032 583 746 731 15 0.020 584 76 74 2 0.026 585 931 912 19 0.020 586 413 404 9 0.022 587 753 735 18 0.024 588 439 424 15 0.034 589 454 439 15 0.033 590 71 62 9 0.127 Imputing summary statistics for 7839 SNPs (not in GWAS and/or SE=0). imputed block 1 imputed block 11 imputed block 21 imputed block 31 imputed block 41 imputed block 51 imputed block 61 imputed block 71 imputed block 81 imputed block 91 imputed block 101 imputed block 111 imputed block 121 imputed block 131 imputed block 141 imputed block 151 imputed block 161 imputed block 171 imputed block 181 imputed block 191 imputed block 201 imputed block 211 imputed block 221 imputed block 231 imputed block 241 imputed block 251 imputed block 261 imputed block 271 imputed block 281 imputed block 291 imputed block 301 imputed block 311 imputed block 321 imputed block 331 imputed block 341 imputed block 351 imputed block 361 imputed block 381 imputed block 391 imputed block 371 imputed block 401 imputed block 411 imputed block 421 imputed block 431 imputed block 441 imputed block 451 imputed block 461 imputed block 481 imputed block 471 imputed block 491 imputed block 501 imputed block 511 imputed block 521 imputed block 541 imputed block 531 imputed block 551 imputed block 561 imputed block 571 imputed block 581 Imputation of summary statistics is completed (time used: 0:0:6). Summary statistics of all SNPs are saved into file [gwas.imputed.ma]. Analysis finished: Sat Jun 6 20:01:05 2026 Computational time: 0:0:8