Mercurial > repos > iuc > last
diff test-data/last_train.txt @ 3:3de2195f32c0 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/last commit 72dc050116d14e7a1342e7f9a2f7e095033d9a3a"
| author | iuc |
|---|---|
| date | Fri, 13 Nov 2020 09:05:49 +0000 |
| parents | 9a7e91fc6562 |
| children | 8705e0d74a0f |
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--- a/test-data/last_train.txt Thu Sep 10 16:08:15 2020 +0000 +++ b/test-data/last_train.txt Fri Nov 13 09:05:49 2020 +0000 @@ -3,493 +3,493 @@ # scale of score parameters: 4.5512 # scale used while training: 91.024 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14901 -# deletes: 694 -# inserts: 834 -# delOpens: 350 -# insOpens: 402 -# alignments: 1 -# mean delete size: 1.98286 -# mean insert size: 2.07463 -# matchProb: 0.951836 -# delOpenProb: 0.0223571 -# insOpenProb: 0.0256787 -# delExtendProb: 0.495677 -# insExtendProb: 0.517986 +# aligned letter pairs: 14938.3 +# deletes: 664.27 +# inserts: 839.49 +# delOpens: 344.82 +# insOpens: 404.93 +# alignments: 3 +# mean delete size: 1.92643 +# mean insert size: 2.07317 +# matchProb: 0.951966 +# delOpenProb: 0.0219742 +# insOpenProb: 0.0258048 +# delExtendProb: 0.480904 +# insExtendProb: 0.517648 -# substitution percent identity: 71.9408 +# substitution percent identity: 71.9318 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3291 532 387 390 -# C 552 3221 180 685 -# G 235 102 1561 84.7 -# T 335 554 146 2651 +# A 3296.3 533.237 387.81 392.24 +# C 553.59 3241.5 182.39 686.22 +# G 232.54 102.399 1565.4 84.91 +# T 335.173 558.68 147.16 2651 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.220773 0.0356887 0.0259615 0.0261627 -# C 0.0370303 0.216077 0.0120751 0.0459525 -# G 0.0157647 0.00684256 0.104718 0.00568201 -# T 0.0224731 0.0371645 0.00979425 0.177839 +# A 0.22048 0.0356667 0.0259395 0.0262358 +# C 0.0370281 0.216815 0.0121996 0.0458993 +# G 0.0155539 0.00684918 0.104705 0.00567939 +# T 0.0224188 0.0373685 0.00984312 0.177318 -# delExistCost: 346 -# insExistCost: 342 -# delExtendCost: 62 +# delExistCost: 343 +# insExistCost: 341 +# delExtendCost: 64 # insExtendCost: 58 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 76 -90 -59 -105 -# C -87 73 -129 -54 -# G -88 -164 145 -167 +# A 76 -90 -59 -104 +# C -87 73 -128 -55 +# G -89 -164 145 -167 # T -112 -66 -127 90 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3148 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14771 -# deletes: 379.3 -# inserts: 567.1 -# delOpens: 185.2 -# insOpens: 246.1 -# alignments: 2 -# mean delete size: 2.04806 -# mean insert size: 2.30435 -# matchProb: 0.971438 -# delOpenProb: 0.01218 -# insOpenProb: 0.0161851 -# delExtendProb: 0.511732 -# insExtendProb: 0.566038 +# aligned letter pairs: 14338.3 +# deletes: 327.44 +# inserts: 474.13 +# delOpens: 166.73 +# insOpens: 216.45 +# alignments: 10 +# mean delete size: 1.96389 +# mean insert size: 2.19048 +# matchProb: 0.973244 +# delOpenProb: 0.0113172 +# insOpenProb: 0.014692 +# delExtendProb: 0.490807 +# insExtendProb: 0.54348 -# substitution percent identity: 70.0105 +# substitution percent identity: 70.6019 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3158 583.4 429.9 391.6 -# C 589 3065 156.8 774 -# G 252.2 88.64 1571 68.46 -# T 342.6 630.1 131.09 2566 +# A 3076.4 546.106 412.41 369.93 +# C 561.42 2983.2 149.401 735.35 +# G 245.82 80.868 1562.07 66.655 +# T 326.724 603.44 120.838 2510.5 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.21341 0.0394248 0.0290516 0.0264634 -# C 0.0398032 0.207126 0.0105962 0.0523051 -# G 0.0170431 0.00599008 0.106165 0.00462637 -# T 0.0231521 0.0425807 0.00885876 0.173404 +# A 0.214366 0.0380532 0.0287371 0.0257771 +# C 0.0391203 0.207872 0.0104104 0.0512399 +# G 0.017129 0.00563496 0.108846 0.00464458 +# T 0.0227664 0.0420483 0.0084201 0.174934 -# delExistCost: 406 -# insExistCost: 400 -# delExtendCost: 60 -# insExtendCost: 51 +# delExistCost: 405 +# insExistCost: 402 +# delExtendCost: 64 +# insExtendCost: 54 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 75 -79 -48 -102 -# C -78 72 -140 -41 -# G -79 -174 146 -185 -# T -107 -52 -136 89 +# A 77 -81 -49 -104 +# C -79 73 -142 -42 +# G -80 -181 146 -186 +# T -108 -52 -142 90 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4973 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14881 -# deletes: 258.8 -# inserts: 446.1 -# delOpens: 112.91 -# insOpens: 168 -# alignments: 2 -# mean delete size: 2.29209 -# mean insert size: 2.65536 -# matchProb: 0.981278 -# delOpenProb: 0.00744548 -# insOpenProb: 0.0110782 -# delExtendProb: 0.563717 -# insExtendProb: 0.623403 +# aligned letter pairs: 14657.7 +# deletes: 218.21 +# inserts: 385.36 +# delOpens: 102.2 +# insOpens: 152.161 +# alignments: 10 +# mean delete size: 2.13513 +# mean insert size: 2.53258 +# matchProb: 0.982218 +# delOpenProb: 0.00684846 +# insOpenProb: 0.0101964 +# delExtendProb: 0.531644 +# insExtendProb: 0.605146 -# substitution percent identity: 68.9366 +# substitution percent identity: 69.4007 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3126 618.3 445 406.6 -# C 622.8 3041 159.4 805.4 -# G 265.2 91.16 1560 68.22 -# T 357.3 660 133.33 2554 +# A 3091.6 591.394 434.35 391.72 +# C 605.8 2996.8 154.6091 779.75 +# G 260.46 83.802 1568.22 67.9713 +# T 351.852 646.07 124.676 2532.5 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.209606 0.0414585 0.0298383 0.0272635 -# C 0.0417602 0.203906 0.0106882 0.054004 -# G 0.0177823 0.0061125 0.104602 0.00457431 -# T 0.0239578 0.0442546 0.0089401 0.171252 +# A 0.210577 0.0402814 0.0295847 0.0266811 +# C 0.0412626 0.20412 0.0105308 0.0531108 +# G 0.0177406 0.00570797 0.106816 0.0046297 +# T 0.0239655 0.0440055 0.008492 0.172495 -# delExistCost: 470 +# delExistCost: 466 # insExistCost: 457 -# delExtendCost: 52 -# insExtendCost: 42 +# delExtendCost: 57 +# insExtendCost: 45 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 75 -73 -44 -99 -# C -73 71 -138 -37 -# G -73 -171 147 -185 -# T -103 -48 -134 88 +# A 76 -75 -45 -100 +# C -73 72 -140 -38 +# G -75 -178 147 -185 +# T -103 -48 -140 89 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5154 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14981 -# deletes: 214.8 -# inserts: 402.9 -# delOpens: 82.32 -# insOpens: 131.98 -# alignments: 2 -# mean delete size: 2.60933 -# mean insert size: 3.05274 -# matchProb: 0.985702 -# delOpenProb: 0.0054164 -# insOpenProb: 0.00868387 -# delExtendProb: 0.61676 -# insExtendProb: 0.672425 +# aligned letter pairs: 14615.5 +# deletes: 176.132 +# inserts: 337.667 +# delOpens: 73.361 +# insOpens: 117.993 +# alignments: 8 +# mean delete size: 2.40089 +# mean insert size: 2.86175 +# matchProb: 0.986477 +# delOpenProb: 0.00495152 +# insOpenProb: 0.00796397 +# delExtendProb: 0.583489 +# insExtendProb: 0.650564 -# substitution percent identity: 68.4035 +# substitution percent identity: 68.8798 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3114 635.9 450 416.3 -# C 640.1 3019 164.9 816.3 -# G 270.6 93.43 1560 69.38 -# T 365.7 670 135.53 2543 +# A 3057.2 603.516 434.56 399.47 +# C 620.42 2962.4 159.336 789.74 +# G 264.31 86.899 1557.17 68.449 +# T 353.847 650 125.897 2508.2 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.208097 0.0424949 0.0300719 0.0278198 -# C 0.0427756 0.201749 0.0110197 0.0545504 -# G 0.0180832 0.00624359 0.104249 0.00463642 -# T 0.0244384 0.0447737 0.00905699 0.16994 +# A 0.208805 0.0412198 0.0296802 0.0272836 +# C 0.0423743 0.20233 0.0108826 0.0539388 +# G 0.0180522 0.00593515 0.106354 0.00467503 +# T 0.0241675 0.0443946 0.00859869 0.171309 -# delExistCost: 518 -# insExistCost: 498 -# delExtendCost: 44 -# insExtendCost: 36 +# delExistCost: 514 +# insExistCost: 497 +# delExtendCost: 49 +# insExtendCost: 39 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -71 -43 -97 -# C -70 71 -135 -36 -# G -71 -169 146 -183 -# T -101 -46 -133 88 +# A 75 -72 -44 -98 +# C -71 72 -137 -37 +# G -73 -174 146 -184 +# T -102 -46 -138 89 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0742 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14981 -# deletes: 197.5 -# inserts: 386.4 -# delOpens: 68.51 -# insOpens: 115.71 -# alignments: 2 -# mean delete size: 2.88279 -# mean insert size: 3.33938 -# matchProb: 0.987657 -# delOpenProb: 0.00451668 -# insOpenProb: 0.00762845 -# delExtendProb: 0.653114 -# insExtendProb: 0.700543 +# aligned letter pairs: 14806.2 +# deletes: 167.925 +# inserts: 326.866 +# delOpens: 62.871 +# insOpens: 105.559 +# alignments: 7 +# mean delete size: 2.67095 +# mean insert size: 3.09652 +# matchProb: 0.988224 +# delOpenProb: 0.00419626 +# insOpenProb: 0.00704543 +# delExtendProb: 0.625601 +# insExtendProb: 0.677057 -# substitution percent identity: 68.1501 +# substitution percent identity: 68.3956 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3103 643.6 451.1 422.5 -# C 649.8 3008 167 819.5 -# G 272.7 94.59 1560 70.43 -# T 369.8 675.4 136.61 2542 +# A 3074.6 626.457 444.21 418.05 +# C 637.55 2977.3 164.69 809.88 +# G 269.41 92.415 1559.3 69.29 +# T 359.136 664.2 129.482 2527.2 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.20706 0.0429467 0.0301014 0.0281929 -# C 0.0433604 0.20072 0.0111437 0.0546843 -# G 0.0181969 0.00631188 0.104097 0.00469971 -# T 0.0246763 0.0450686 0.00911582 0.169625 +# A 0.207419 0.042262 0.0299673 0.0282025 +# C 0.0430104 0.200854 0.0111103 0.0546361 +# G 0.0181749 0.0062345 0.105193 0.00467444 +# T 0.024228 0.0448082 0.00873511 0.17049 + +# delExistCost: 546 +# insExistCost: 519 +# delExtendCost: 42 +# insExtendCost: 35 + +# score matrix (query letters = columns, reference letters = rows): +# A C G T +# A 75 -70 -43 -95 +# C -69 71 -134 -36 +# G -71 -169 146 -183 +# T -101 -45 -136 88 + +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1177 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# delExistCost: 549 -# insExistCost: 522 -# delExtendCost: 39 +# aligned letter pairs: 14896.9 +# deletes: 177.451 +# inserts: 344.879 +# delOpens: 59.29 +# insOpens: 103.311 +# alignments: 5 +# mean delete size: 2.99293 +# mean insert size: 3.33826 +# matchProb: 0.988809 +# delOpenProb: 0.00393548 +# insOpenProb: 0.00685746 +# delExtendProb: 0.66588 +# insExtendProb: 0.700443 + +# substitution percent identity: 68.1858 + +# count matrix (query letters = columns, reference letters = rows): +# A C G T +# A 3084.6 635.337 445.51 422.24 +# C 649.18 2997.2 169.11 816.24 +# G 273.53 93.848 1562.4 71.64 +# T 365.354 674.15 132.032 2532.3 + +# probability matrix (query letters = columns, reference letters = rows): +# A C G T +# A 0.206678 0.0425696 0.0298506 0.0282914 +# C 0.0434971 0.200822 0.0113309 0.0546907 +# G 0.0183274 0.00628811 0.104686 0.00480011 +# T 0.0244799 0.0451702 0.00884656 0.169672 + +# delExistCost: 567 +# insExistCost: 531 +# delExtendCost: 37 # insExtendCost: 32 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -43 -95 -# C -68 70 -134 -35 -# G -71 -168 146 -182 -# T -100 -45 -132 88 +# A 75 -70 -43 -95 +# C -68 71 -132 -35 +# G -70 -168 146 -181 +# T -100 -45 -135 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7441 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5512 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14981 -# deletes: 192.1 -# inserts: 380.9 -# delOpens: 62.34 -# insOpens: 108.21 -# alignments: 2 -# mean delete size: 3.08149 -# mean insert size: 3.52001 -# matchProb: 0.988548 -# delOpenProb: 0.00411362 -# insOpenProb: 0.00714043 -# delExtendProb: 0.675482 -# insExtendProb: 0.71591 +# aligned letter pairs: 14897.4 +# deletes: 183.45 +# inserts: 350.682 +# delOpens: 57.728 +# insOpens: 101.786 +# alignments: 5 +# mean delete size: 3.17783 +# mean insert size: 3.44529 +# matchProb: 0.989012 +# delOpenProb: 0.00383246 +# insOpenProb: 0.00675739 +# delExtendProb: 0.68532 +# insExtendProb: 0.709748 -# substitution percent identity: 67.9883 +# substitution percent identity: 68.1676 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3093 648 451.1 425.7 -# C 654.2 3008 169 821.5 -# G 272.8 95.26 1550 71.05 -# T 371.8 677.5 136.66 2532 +# A 3083.6 635.04 445.71 423.87 +# C 650.27 2996.2 169.49 816.21 +# G 272.96 94.054 1562.4 71.81 +# T 365.777 674.06 132.018 2532.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.206509 0.0432647 0.0301184 0.0284225 -# C 0.0436786 0.200834 0.0112835 0.0548487 -# G 0.0182139 0.00636018 0.103488 0.00474376 -# T 0.0248238 0.0452343 0.00912431 0.169053 +# A 0.206594 0.0425463 0.0298616 0.0283983 +# C 0.0435666 0.200739 0.0113555 0.0546843 +# G 0.0182877 0.00630141 0.104677 0.00481111 +# T 0.0245062 0.0451605 0.00884491 0.169665 + +# delExistCost: 578 +# insExistCost: 536 +# delExtendCost: 34 +# insExtendCost: 31 + +# score matrix (query letters = columns, reference letters = rows): +# A C G T +# A 75 -70 -43 -94 +# C -68 71 -132 -36 +# G -71 -168 146 -180 +# T -100 -45 -135 88 + +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3765 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# delExistCost: 566 -# insExistCost: 534 -# delExtendCost: 36 +# aligned letter pairs: 14897.3 +# deletes: 186.949 +# inserts: 354.265 +# delOpens: 56.756 +# insOpens: 101.214 +# alignments: 5 +# mean delete size: 3.29391 +# mean insert size: 3.50016 +# matchProb: 0.989113 +# delOpenProb: 0.00376834 +# insOpenProb: 0.00672015 +# delExtendProb: 0.696409 +# insExtendProb: 0.714299 + +# substitution percent identity: 68.1476 + +# count matrix (query letters = columns, reference letters = rows): +# A C G T +# A 3081.6 633.831 445.71 424.07 +# C 650.26 2986.2 169.38 816.09 +# G 272.84 94.051 1561.4 71.9 +# T 365.569 674.07 131.791 2532.4 + +# probability matrix (query letters = columns, reference letters = rows): +# A C G T +# A 0.206664 0.0425072 0.029891 0.0284398 +# C 0.0436089 0.200266 0.0113593 0.0547301 +# G 0.0182977 0.00630742 0.104714 0.00482189 +# T 0.0245165 0.0452057 0.00883841 0.169833 + +# delExistCost: 584 +# insExistCost: 539 +# delExtendCost: 33 # insExtendCost: 30 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -42 -94 -# C -68 70 -133 -35 -# G -70 -167 147 -181 -# T -99 -45 -131 88 +# A 75 -70 -43 -94 +# C -68 71 -132 -35 +# G -71 -168 146 -180 +# T -100 -45 -135 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2473 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.5205 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14981 -# deletes: 194.5 -# inserts: 383.3 -# delOpens: 60.42 -# insOpens: 106.36 -# alignments: 2 -# mean delete size: 3.21913 -# mean insert size: 3.6038 -# matchProb: 0.988794 -# delOpenProb: 0.00398791 -# insOpenProb: 0.0070201 -# delExtendProb: 0.689357 -# insExtendProb: 0.722515 +# aligned letter pairs: 14897.4 +# deletes: 188.951 +# inserts: 357.176 +# delOpens: 56.362 +# insOpens: 100.973 +# alignments: 5 +# mean delete size: 3.35245 +# mean insert size: 3.53734 +# matchProb: 0.989155 +# delOpenProb: 0.00374231 +# insOpenProb: 0.00670439 +# delExtendProb: 0.701711 +# insExtendProb: 0.717302 -# substitution percent identity: 67.9593 +# substitution percent identity: 68.1403 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3093 648.9 451.2 426.7 -# C 655.2 3008 169 821.4 -# G 273.8 95.46 1550 71.26 -# T 372.8 678.6 136.64 2532 +# A 3081.6 634.732 445.81 423.98 +# C 650.18 2986.2 169.39 816.1 +# G 273.05 94.134 1561.4 71.9 +# T 365.574 674.07 131.782 2531.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.206421 0.0433063 0.0301122 0.0284771 -# C 0.0437268 0.200748 0.0112787 0.0548186 -# G 0.0182729 0.00637081 0.103444 0.00475575 -# T 0.0248799 0.0452884 0.00911908 0.168981 +# A 0.206662 0.0425672 0.0298975 0.0284335 +# C 0.0436032 0.200264 0.0113598 0.0547303 +# G 0.0183116 0.00631293 0.104713 0.00482185 +# T 0.0245166 0.0452053 0.00883773 0.169764 -# delExistCost: 575 -# insExistCost: 539 -# delExtendCost: 34 -# insExtendCost: 29 +# delExistCost: 587 +# insExistCost: 541 +# delExtendCost: 32 +# insExtendCost: 30 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -42 -94 -# C -68 70 -132 -35 -# G -70 -167 147 -180 -# T -99 -45 -131 88 - -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2311 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# A 75 -70 -43 -94 +# C -68 71 -132 -35 +# G -71 -168 146 -180 +# T -100 -45 -135 88 -# aligned letter pairs: 14981 -# deletes: 196.9 -# inserts: 385.7 -# delOpens: 59.47 -# insOpens: 105.68 -# alignments: 2 -# mean delete size: 3.31091 -# mean insert size: 3.6497 -# matchProb: 0.9889 -# delOpenProb: 0.00392563 -# insOpenProb: 0.00697597 -# delExtendProb: 0.697969 -# insExtendProb: 0.726005 - -# substitution percent identity: 67.9572 - -# count matrix (query letters = columns, reference letters = rows): -# A C G T -# A 3093 648.8 451.2 426.6 -# C 655.1 3008 169.9 821.4 -# G 273.8 95.45 1550 71.26 -# T 372.7 678.6 136.63 2532 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4821 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# probability matrix (query letters = columns, reference letters = rows): -# A C G T -# A 0.206414 0.0432982 0.0301112 0.0284695 -# C 0.0437187 0.200742 0.0113384 0.0548169 -# G 0.0182723 0.00636994 0.103441 0.0047556 -# T 0.0248725 0.045287 0.00911813 0.168975 - -# delExistCost: 580 -# insExistCost: 541 -# delExtendCost: 33 -# insExtendCost: 29 +# aligned letter pairs: 14897.4 +# deletes: 189.355 +# inserts: 357.265 +# delOpens: 56.08 +# insOpens: 100.658 +# alignments: 5 +# mean delete size: 3.37652 +# mean insert size: 3.5493 +# matchProb: 0.989194 +# delOpenProb: 0.00372374 +# insOpenProb: 0.00668374 +# delExtendProb: 0.703837 +# insExtendProb: 0.718254 -# score matrix (query letters = columns, reference letters = rows): -# A C G T -# A 74 -69 -42 -94 -# C -68 70 -132 -35 -# G -70 -167 147 -180 -# T -99 -45 -131 88 - -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1656 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB - -# aligned letter pairs: 14981 -# deletes: 197 -# inserts: 385.7 -# delOpens: 58.72 -# insOpens: 105.14 -# alignments: 2 -# mean delete size: 3.3549 -# mean insert size: 3.66844 -# matchProb: 0.988985 -# delOpenProb: 0.00387646 -# insOpenProb: 0.00694091 -# delExtendProb: 0.701929 -# insExtendProb: 0.727405 - -# substitution percent identity: 67.9308 +# substitution percent identity: 68.1453 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3093 648.8 451.2 426.6 -# C 656 2998 169.9 821.4 -# G 273.8 95.55 1550 71.36 -# T 372.7 678.6 136.62 2532 - -# probability matrix (query letters = columns, reference letters = rows): -# A C G T -# A 0.206537 0.043324 0.0301292 0.0284865 -# C 0.0438048 0.200193 0.0113452 0.0548495 -# G 0.0182832 0.00638041 0.103502 0.00476511 -# T 0.0248873 0.0453139 0.00912288 0.169076 - -# delExistCost: 584 -# insExistCost: 542 -# delExtendCost: 32 -# insExtendCost: 29 - -# score matrix (query letters = columns, reference letters = rows): -# A C G T -# A 74 -69 -42 -94 -# C -68 70 -132 -35 -# G -70 -166 146 -180 -# T -99 -45 -132 88 - -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB - -# aligned letter pairs: 14981 -# deletes: 197 -# inserts: 384.7 -# delOpens: 57.97 -# insOpens: 104.51 -# alignments: 2 -# mean delete size: 3.39831 -# mean insert size: 3.68099 -# matchProb: 0.989075 -# delOpenProb: 0.00382729 -# insOpenProb: 0.00689995 -# delExtendProb: 0.705736 -# insExtendProb: 0.728334 - -# substitution percent identity: 67.93 - -# count matrix (query letters = columns, reference letters = rows): -# A C G T -# A 3093 648.8 451.2 427.6 -# C 656 2998 169.9 821.4 -# G 273.8 95.75 1550 71.36 -# T 372.7 678.6 135.61 2532 +# A 3081.6 633.731 445.81 423.98 +# C 650.08 2986.2 169.39 816.1 +# G 273.05 94.136 1561.4 71.9 +# T 365.674 674.07 131.672 2531.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.206534 0.0433235 0.0301288 0.0285529 -# C 0.0438042 0.200191 0.011345 0.0548488 -# G 0.0182829 0.00639368 0.103501 0.00476505 -# T 0.024887 0.0453133 0.00905532 0.169074 +# A 0.206677 0.0425032 0.0298997 0.0284356 +# C 0.0435997 0.200279 0.0113607 0.0547344 +# G 0.018313 0.00631353 0.10472 0.0048222 +# T 0.0245251 0.0452087 0.00883101 0.169776 -# delExistCost: 586 -# insExistCost: 543 +# delExistCost: 588 +# insExistCost: 541 # delExtendCost: 32 -# insExtendCost: 29 +# insExtendCost: 30 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -42 -94 -# C -68 70 -132 -35 -# G -70 -166 147 -180 -# T -99 -45 -132 88 +# A 75 -70 -43 -94 +# C -68 71 -132 -35 +# G -71 -168 146 -180 +# T -100 -45 -135 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/rdallet/galaxy/tools/last/test-data/humdb /tmp/tmpow095T/tmp/tmpmqx0kk84 -# aligned letter pairs: 14981 -# deletes: 196 -# inserts: 384.7 -# delOpens: 57.87 -# insOpens: 104.51 -# alignments: 2 -# mean delete size: 3.3869 -# mean insert size: 3.68099 -# matchProb: 0.989081 -# delOpenProb: 0.00382071 -# insOpenProb: 0.0069 -# delExtendProb: 0.704745 -# insExtendProb: 0.728334 +# aligned letter pairs: 14897.4 +# deletes: 188.951 +# inserts: 356.964 +# delOpens: 55.8286 +# insOpens: 100.647 +# alignments: 5 +# mean delete size: 3.38448 +# mean insert size: 3.54669 +# matchProb: 0.989211 +# delOpenProb: 0.00370711 +# insOpenProb: 0.00668312 +# delExtendProb: 0.704534 +# insExtendProb: 0.718047 -# substitution percent identity: 67.93 +# substitution percent identity: 68.1409 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3093 648.8 451.2 427.6 -# C 656 2998 169.9 821.4 -# G 273.8 95.75 1550 71.36 -# T 372.7 678.6 135.61 2532 +# A 3081.6 633.731 445.81 424.08 +# C 650.28 2986.2 169.49 816.1 +# G 273.05 94.136 1561.4 71.9 +# T 365.673 674.17 131.672 2530.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# A 0.206534 0.0433235 0.0301288 0.0285529 -# C 0.0438042 0.200191 0.011345 0.0548488 -# G 0.0182829 0.00639368 0.103501 0.00476505 -# T 0.024887 0.0453133 0.00905532 0.169074 +# A 0.206684 0.0425046 0.0299007 0.0284432 +# C 0.0436146 0.200286 0.0113678 0.0547362 +# G 0.0183136 0.00631375 0.104724 0.00482237 +# T 0.0245259 0.0452169 0.0088313 0.169715 -# delExistCost: 586 -# insExistCost: 543 +# delExistCost: 588 +# insExistCost: 541 # delExtendCost: 32 -# insExtendCost: 29 +# insExtendCost: 30 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -42 -94 -# C -68 70 -132 -35 -# G -70 -166 147 -180 -# T -99 -45 -132 88 +# A 75 -70 -43 -94 +# C -68 71 -132 -35 +# G -71 -168 146 -180 +# T -100 -45 -135 88 #last -X 0 #last -Q 0 -#last -t4.80115 +#last -t4.72795 #last -a 29 #last -A 28 #last -b 2 @@ -500,5 +500,5 @@ A C G T A 4 -3 -2 -5 C -3 4 -7 -2 -G -3 -8 7 -9 +G -4 -8 7 -9 T -5 -2 -7 4