@@ -348,7 +353,7 @@ - + @@ -369,7 +374,7 @@ - +

diff -r 3de2195f32c0 -r 8705e0d74a0f lastdb.xml --- a/lastdb.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lastdb.xml Wed Mar 24 22:36:50 2021 +0000 @@ -1,4 +1,4 @@ - + prepares sequences for subsequent comparison and alignment using lastal. @@ -11,15 +11,22 @@ - +

@@ -81,7 +90,7 @@ - + @@ -134,7 +143,7 @@ - +

@@ -145,7 +154,7 @@ - + @@ -159,6 +168,10 @@

+ + +

@@ -170,7 +183,7 @@ - +

@@ -182,7 +195,7 @@ - + diff -r 3de2195f32c0 -r 8705e0d74a0f lastsplit.xml --- a/lastsplit.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lastsplit.xml Wed Mar 24 22:36:50 2021 +0000 @@ -1,4 +1,4 @@ - + finds "split alignments" (typically for DNA) or "spliced alignments" (typically for RNA). @@ -72,7 +72,7 @@ - + diff -r 3de2195f32c0 -r 8705e0d74a0f lasttrain.xml --- a/lasttrain.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/lasttrain.xml Wed Mar 24 22:36:50 2021 +0000 @@ -1,4 +1,4 @@ - + finds the rates (probabilities) of insertion, deletion, and substitutions between two sets of sequences. @@ -11,11 +11,16 @@ '$outfile' ]]> - + @@ -115,15 +118,15 @@

- - + + - + diff -r 3de2195f32c0 -r 8705e0d74a0f macros_last.xml --- a/macros_last.xml Fri Nov 13 09:05:49 2020 +0000 +++ b/macros_last.xml Wed Mar 24 22:36:50 2021 +0000 @@ -1,5 +1,5 @@ - 1021 + 1205 + read MAF-format alignments and write them in another format. diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/fuguMito.fa.gz Binary file test-data/fuguMito.fa.gz has changed diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/fuguMito.fq.gz Binary file test-data/fuguMito.fq.gz has changed diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/humanMito.fa.gz Binary file test-data/humanMito.fa.gz has changed diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/humanMito.fq.gz Binary file test-data/humanMito.fq.gz has changed diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_fastq.maf --- a/test-data/last_align_fastq.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_fastq.maf Wed Mar 24 22:36:50 2021 +0000 @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=1 -# db_files/lastdb +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb-sanger # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_gen.maf --- a/test-data/last_align_gen.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_gen.maf Wed Mar 24 22:36:50 2021 +0000 @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_align_prot.maf --- a/test-data/last_align_prot.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_align_prot.maf Wed Mar 24 22:36:50 2021 +0000 @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=11 b=2 A=11 B=2 e=22 d=13 x=21 y=9 z=21 D=1e+06 E=2.73494e+09 # R=10 u=0 s=1 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=3.08611 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/hedgdb # Reference sequences=1 normal letters=411 # lambda=0.305935 K=0.102404 # @@ -39,28 +39,4 @@ # name start alnSize strand seqSize alignment # # batch 0 -a score=729 EG2=1.4e-80 E=1.2e-101 -s NP_002172.2 13 264 + 411 LVLLLLLVVPA----AWGCGPGRVVGSRRRPPRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKSEHSAAAKTGGCFPAGAQVRLESGARVALSAVRPGDRVLAMGEDGSPTFSDVLIFLDREPHRLRAFQVIETQDPPRRLALTPAHLL -s NP_001034065.1 66 265 + 471 LVALLLIVLPMVFSPAHSCGPGRGLGRHRA--RNLYPLVLKQTIPNLSEYTNSASGPLEGVIRRDSPKFKDLVPNYNRDILFRDEEGTGADRLMSKRCKEKLNVLAYSVMNEWPGIRLLVTESWDEDYHHGQESLHYEGRAVTIATSDRDQSKYGMLARLAVEAGFDWVSYVSRRHIYCSVKSDSSISSHVHGCFTPESTALLESGVRKPLGELSIGDRVLSMTANGQAVYSEVILFMDRNLEQMQNFVQLHT-DGGAVLTVTPAHLV - -a score=131 EG2=0.4 E=4.1e-14 -s NP_002172.2 293 95 + 411 FASHVQPGQYVLVAGVPG--LQPARVAAVSTHVALGAYAPLTKHGTLVVEDVVASCFAAVADHHLAQLAFWPLRLFHSLAWGSWTPG-EGVHWYPQLL -s NP_001034065.1 344 96 + 471 FADRIEEKNQVLVRDVETGELRPQRVVKVGSVRSKGVVAPLTREGTIVVNSVAASCYAVINSQSLAHWGLAPMRLLSTLE--AWLPAKEQLHSSPKVV - -a score=41 EG2=3.7e+11 E=0.06 -s NP_002172.2 91 34 + 411 KDEENTGADRLMTQRCKDRLNSLAISVMNQWPGV -s NP_001034065.1 44 34 + 471 QEETQTMRHIAHTQRCLSRLTSLVALLLIVLPMV - -a score=30 EG2=1.1e+13 E=1.8 -s NP_002172.2 180 18 + 411 ESKAHVHCSVKSEHSAAA -s NP_001034065.1 20 18 + 471 DAKCHSSSSSSSSKSAAS - -a score=24 EG2=6.6e+13 E=12 -s NP_002172.2 26 23 + 411 GCGPGRVVGSRRRPPRKLVPLAY -s NP_001034065.1 150 21 + 471 GTGADRLMSKRCK--EKLNVLAY - -a score=24 EG2=6.6e+13 E=12 -s NP_002172.2 106 27 + 411 CKDRLNSLAISVMNQWPGVKLRVTEGW -s NP_001034065.1 399 27 + 471 CYAVINSQSLAHWGLAPMRLLSTLEAW - # Query sequences=1 diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_split.maf --- a/test-data/last_split.maf Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_split.maf Wed Mar 24 22:36:50 2021 +0000 @@ -1,8 +1,8 @@ -# LAST version 1021 +# LAST version 1205 # # a=7 b=1 A=7 B=1 e=22 d=13 x=21 y=9 z=21 D=1e+06 # R=10 u=0 s=2 S=0 M=0 T=0 m=10 l=1 L=999999999 n=10 k=1 w=1000 t=2.82533 j=3 Q=0 -# ref_db +# /home/berntm/.planemo/planemo_tmp_3z8peizh/test-data/humdb # Reference sequences=1 normal letters=16571 # # A R N D C Q E G H I L K M F P S T W Y V B J Z X * @@ -89,7 +89,7 @@ s fuguMito 16146 196 + 16447 A-----GTGC---AGCGC-----GTCAATGGTTCA-TCAAGGTTGAA-CAT---TTTTTCT-TGGTTTATGGTA---ATGTTAATTAATGAATTAAGACAT---TATTTAAG------AATTACATTACTGATATCAAGGACATAA--ATAATAATACGAT-TCAACAATCATACAATTTCAcccccttcttctttttaaaaaaatt-aacgtataccccccctacccccc p 333333336?????@@@@@@@@@@@@@@@@@@@@@@@@@@@@AAAAAABBBBBBCCDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDEEEEEEEEEEEEEEEEEEEEEEDEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEED@@: -a score=255 mismap=0.516 acc=AG +a score=255 mismap=0.515 acc=AG s humanMito 2030 114 + 16571 ATAGAATCTTAGTTCAA-CTTTAAATTTG-CCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTGGACACTAGGA-AAAAACCTTGTA s fuguMito 16342 104 + 16447 ctaAAAAATAGGAGAGACCTTTAAGTTTGAACCA-AG----CTCT----CCActt----aattaaatattcatcatattattatcatatattataatattataataatataattata p ##################################################################################################################### diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_train.txt --- a/test-data/last_train.txt Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_train.txt Wed Mar 24 22:36:50 2021 +0000 @@ -1,43 +1,43 @@ -# lastal version: 1021 +# lastal version: 1205 # maximum percent identity: 100 # scale of score parameters: 4.5512 # scale used while training: 91.024 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14938.3 -# deletes: 664.27 -# inserts: 839.49 -# delOpens: 344.82 -# insOpens: 404.93 +# aligned letter pairs: 14938.4 +# deletes: 664.28 +# inserts: 839.52 +# delOpens: 344.93 +# insOpens: 404.94 # 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 +# mean delete size: 1.92584 +# mean insert size: 2.0732 +# matchProb: 0.951959 +# delOpenProb: 0.0219809 +# insOpenProb: 0.0258051 +# delExtendProb: 0.480746 +# insExtendProb: 0.517653 -# substitution percent identity: 71.9318 +# substitution percent identity: 71.9301 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3296.3 533.242 387.82 392.35 +# C 553.59 3241.5 182.39 686.23 +# G 232.64 102.401 1565.4 84.91 +# T 335.174 558.781 147.17 2651 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.220475 0.0356662 0.0259396 0.0262426 +# C 0.0370272 0.21681 0.0121993 0.0458989 +# G 0.0155603 0.00684915 0.104703 0.00567926 +# T 0.0224183 0.0373744 0.00984356 0.177314 -# delExistCost: 343 +# delExistCost: 342 # insExistCost: 341 -# delExtendCost: 64 +# delExtendCost: 65 # insExtendCost: 58 # score matrix (query letters = columns, reference letters = rows): @@ -47,84 +47,84 @@ # G -89 -164 145 -167 # T -112 -66 -127 90 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1872 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14338.3 -# deletes: 327.44 -# inserts: 474.13 -# delOpens: 166.73 -# insOpens: 216.45 +# aligned letter pairs: 14397.9 +# deletes: 322.93 +# inserts: 481.67 +# delOpens: 166.26 +# insOpens: 218.88 # 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 +# mean delete size: 1.94232 +# mean insert size: 2.20061 +# matchProb: 0.973223 +# delOpenProb: 0.0112383 +# insOpenProb: 0.0147951 +# delExtendProb: 0.485152 +# insExtendProb: 0.545581 -# substitution percent identity: 70.6019 +# substitution percent identity: 70.5263 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3087.2 550.976 415.27 370.69 +# C 567.6 2996 150.293 740.47 +# G 246.31 81.558 1563.06 66.884 +# T 329.603 608.12 121.409 2521.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.214138 0.0382175 0.0288045 0.0257123 +# C 0.0393706 0.207812 0.0104248 0.0513615 +# G 0.0170849 0.00565713 0.108419 0.0046393 +# T 0.0228624 0.0421812 0.00842133 0.174893 -# delExistCost: 405 -# insExistCost: 402 -# delExtendCost: 64 +# delExistCost: 404 +# insExistCost: 401 +# delExtendCost: 65 # insExtendCost: 54 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 77 -81 -49 -104 -# C -79 73 -142 -42 -# G -80 -181 146 -186 -# T -108 -52 -142 90 +# A 76 -81 -49 -104 +# C -78 73 -142 -42 +# G -79 -180 146 -186 +# T -108 -52 -141 89 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.4093 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14657.7 -# deletes: 218.21 -# inserts: 385.36 -# delOpens: 102.2 -# insOpens: 152.161 +# aligned letter pairs: 14586.1 +# deletes: 207.97 +# inserts: 370.61 +# delOpens: 97.51 +# insOpens: 146.118 # 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 +# mean delete size: 2.13281 +# mean insert size: 2.53637 +# matchProb: 0.982843 +# delOpenProb: 0.00657043 +# insOpenProb: 0.00984574 +# delExtendProb: 0.531134 +# insExtendProb: 0.605736 -# substitution percent identity: 69.4007 +# substitution percent identity: 69.4001 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3071.2 586.39 432.58 390.03 +# C 602.06 2979.4 154.2015 775.84 +# G 260.13 83.439 1563.17 67.5164 +# T 349.003 643.71 124.293 2522.3 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.21028 0.0401492 0.0296181 0.0267048 +# C 0.0412221 0.203995 0.0105579 0.0531206 +# G 0.0178107 0.00571294 0.107028 0.00462274 +# T 0.0238957 0.0440738 0.00851015 0.172698 -# delExistCost: 466 -# insExistCost: 457 +# delExistCost: 469 +# insExistCost: 460 # delExtendCost: 57 # insExtendCost: 45 @@ -132,175 +132,175 @@ # A C G T # A 76 -75 -45 -100 # C -73 72 -140 -38 -# G -75 -178 147 -185 +# G -74 -178 147 -185 # T -103 -48 -140 89 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4064 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14615.5 -# deletes: 176.132 -# inserts: 337.667 -# delOpens: 73.361 -# insOpens: 117.993 +# aligned letter pairs: 14614.3 +# deletes: 173.005 +# inserts: 333.783 +# delOpens: 71.881 +# insOpens: 116.037 # 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 +# mean delete size: 2.40683 +# mean insert size: 2.87652 +# matchProb: 0.986705 +# delOpenProb: 0.00485315 +# insOpenProb: 0.0078344 +# delExtendProb: 0.584515 +# insExtendProb: 0.652358 -# substitution percent identity: 68.8798 +# substitution percent identity: 68.8464 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3054 603.416 435.41 400.71 +# C 620.59 2961.2 159.53 789.72 +# G 265.6 86.864 1557.13 68.4163 +# T 354.125 649.76 125.994 2505.1 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.208641 0.0412238 0.0297461 0.0273755 +# C 0.0423971 0.202301 0.0108987 0.0539516 +# G 0.0181451 0.00593432 0.106379 0.00467402 +# T 0.0241929 0.0443899 0.00860758 0.171142 -# delExistCost: 514 -# insExistCost: 497 +# delExistCost: 516 +# insExistCost: 500 # delExtendCost: 49 -# insExtendCost: 39 +# insExtendCost: 38 # score matrix (query letters = columns, reference letters = rows): # A C G T # A 75 -72 -44 -98 -# C -71 72 -137 -37 -# G -73 -174 146 -184 +# C -70 72 -136 -37 +# G -72 -174 146 -184 # T -102 -46 -138 89 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2552 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14806.2 -# deletes: 167.925 -# inserts: 326.866 -# delOpens: 62.871 -# insOpens: 105.559 +# aligned letter pairs: 14846.5 +# deletes: 168.42 +# inserts: 340.671 +# delOpens: 63.085 +# insOpens: 107.237 # 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 +# mean delete size: 2.66973 +# mean insert size: 3.1768 +# matchProb: 0.988132 +# delOpenProb: 0.00419872 +# insOpenProb: 0.00713732 +# delExtendProb: 0.62543 +# insExtendProb: 0.685218 -# substitution percent identity: 68.3956 +# substitution percent identity: 68.3619 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3085.6 630.559 444.71 420.06 +# C 641.49 2985.3 165.39 812.21 +# G 270.72 92.7 1563.4 69.63 +# T 360.446 667.21 130.014 2532.3 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.207481 0.0423998 0.029903 0.0282455 +# C 0.0431348 0.200736 0.0111211 0.0546143 +# G 0.0182037 0.0062333 0.105126 0.00468203 +# T 0.024237 0.0448643 0.00874235 0.170276 # delExistCost: 546 -# insExistCost: 519 +# insExistCost: 521 # delExtendCost: 42 -# insExtendCost: 35 +# insExtendCost: 34 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 75 -70 -43 -95 +# A 75 -70 -44 -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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0533 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14896.9 -# deletes: 177.451 -# inserts: 344.879 -# delOpens: 59.29 -# insOpens: 103.311 +# aligned letter pairs: 14896.8 +# deletes: 179.049 +# inserts: 347.285 +# delOpens: 59.728 +# insOpens: 103.021 # 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 +# mean delete size: 2.99774 +# mean insert size: 3.37101 +# matchProb: 0.988799 +# delOpenProb: 0.00396454 +# insOpenProb: 0.00683818 +# delExtendProb: 0.666415 +# insExtendProb: 0.703353 -# substitution percent identity: 68.1858 +# substitution percent identity: 68.1898 # 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 +# A 3083.6 634.137 445.41 422.54 +# C 648.98 2997.2 169.11 816.24 +# G 273.63 93.839 1562.4 71.58 +# T 365.254 674.05 132.042 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 +# A 0.206644 0.0424959 0.0298486 0.028316 +# C 0.0434906 0.200854 0.0113327 0.0546993 +# G 0.018337 0.0062885 0.104702 0.00479684 +# T 0.024477 0.0451706 0.00884863 0.169699 -# delExistCost: 567 -# insExistCost: 531 +# delExistCost: 566 +# insExistCost: 532 # delExtendCost: 37 # insExtendCost: 32 # score matrix (query letters = columns, reference letters = rows): # A C G T # A 75 -70 -43 -95 -# C -68 71 -132 -35 +# C -68 71 -132 -36 # G -70 -168 146 -181 # T -100 -45 -135 88 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3763 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco -# aligned letter pairs: 14897.4 -# deletes: 183.45 -# inserts: 350.682 -# delOpens: 57.728 -# insOpens: 101.786 +# aligned letter pairs: 14897.3 +# deletes: 182.446 +# inserts: 350.271 +# delOpens: 57.786 +# insOpens: 101.442 # 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 +# mean delete size: 3.15727 +# mean insert size: 3.45292 +# matchProb: 0.989031 +# delOpenProb: 0.00383641 +# insOpenProb: 0.00673473 +# delExtendProb: 0.683271 +# insExtendProb: 0.71039 -# substitution percent identity: 68.1676 +# substitution percent identity: 68.1657 # count matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 3083.6 635.136 445.71 423.86 +# C 650.36 2996.2 169.48 816.19 +# G 272.95 94.064 1561.4 71.9 +# T 365.571 674.06 131.918 2532.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.206609 0.0425557 0.0298637 0.0283997 +# C 0.0435758 0.200753 0.0113556 0.0546868 +# G 0.0182884 0.00630253 0.104618 0.00481749 +# T 0.0244942 0.0451638 0.00883885 0.169677 -# delExistCost: 578 -# insExistCost: 536 +# delExistCost: 577 +# insExistCost: 537 # delExtendCost: 34 # insExtendCost: 31 @@ -311,40 +311,40 @@ # 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.3676 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco # aligned letter pairs: 14897.3 -# deletes: 186.949 -# inserts: 354.265 -# delOpens: 56.756 -# insOpens: 101.214 +# deletes: 186.95 +# inserts: 354.262 +# delOpens: 56.767 +# insOpens: 100.893 # 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 +# mean delete size: 3.29329 +# mean insert size: 3.51126 +# matchProb: 0.989133 +# delOpenProb: 0.00376915 +# insOpenProb: 0.00669898 +# delExtendProb: 0.696352 +# insExtendProb: 0.715202 -# substitution percent identity: 68.1476 +# substitution percent identity: 68.1477 # 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 +# C 650.26 2986.2 169.38 816.08 # G 272.84 94.051 1561.4 71.9 -# T 365.569 674.07 131.791 2532.4 +# T 365.569 674.17 131.691 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 +# A 0.206664 0.0425072 0.0298911 0.0284398 +# C 0.043609 0.200266 0.0113593 0.0547295 +# G 0.0182977 0.00630743 0.104714 0.00482189 +# T 0.0245165 0.0452125 0.00883171 0.169833 -# delExistCost: 584 -# insExistCost: 539 +# delExistCost: 583 +# insExistCost: 540 # delExtendCost: 33 # insExtendCost: 30 @@ -355,39 +355,39 @@ # G -71 -168 146 -180 # T -100 -45 -135 88 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.511 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco # aligned letter pairs: 14897.4 -# deletes: 188.951 -# inserts: 357.176 -# delOpens: 56.362 -# insOpens: 100.973 +# deletes: 188.952 +# inserts: 357.073 +# delOpens: 56.483 +# insOpens: 100.742 # 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 +# mean delete size: 3.34529 +# mean insert size: 3.54443 +# matchProb: 0.989162 +# delOpenProb: 0.00375038 +# insOpenProb: 0.0066891 +# delExtendProb: 0.701072 +# insExtendProb: 0.717867 -# substitution percent identity: 68.1403 +# substitution percent identity: 68.1444 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3081.6 634.732 445.81 423.98 +# A 3081.6 633.732 445.81 423.98 # 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 +# T 365.574 674.17 131.782 2531.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.206675 0.0425027 0.0298993 0.0284352 +# C 0.0436058 0.200276 0.0113605 0.0547336 +# G 0.0183127 0.00631331 0.104719 0.00482214 +# T 0.0245181 0.0452147 0.00883826 0.169774 -# delExistCost: 587 +# delExistCost: 586 # insExistCost: 541 # delExtendCost: 32 # insExtendCost: 30 @@ -399,37 +399,37 @@ # G -71 -168 146 -180 # T -100 -45 -135 88 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.494 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco # aligned letter pairs: 14897.4 -# deletes: 189.355 -# inserts: 357.265 -# delOpens: 56.08 -# insOpens: 100.658 +# deletes: 190.558 +# inserts: 358.367 +# delOpens: 56.231 +# insOpens: 100.769 # 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 +# mean delete size: 3.38884 +# mean insert size: 3.55632 +# matchProb: 0.989177 +# delOpenProb: 0.0037337 +# insOpenProb: 0.00669099 +# delExtendProb: 0.704914 +# insExtendProb: 0.718811 -# substitution percent identity: 68.1453 +# substitution percent identity: 68.1458 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3081.6 633.731 445.81 423.98 +# A 3081.6 633.732 445.81 423.98 # 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 +# G 273.05 94.125 1561.4 71.9 +# T 365.574 674.07 131.672 2531.4 # probability matrix (query letters = columns, reference letters = rows): # A C G T -# 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 +# A 0.206679 0.0425036 0.0298999 0.0284358 +# C 0.0436 0.200281 0.0113608 0.0547348 +# G 0.0183131 0.00631284 0.104721 0.00482224 +# T 0.0245186 0.045209 0.00883107 0.169778 # delExistCost: 588 # insExistCost: 541 @@ -443,7 +443,7 @@ # G -71 -168 146 -180 # T -100 -45 -135 88 -# 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 +# lastal -j7 -D1000000 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4704 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpc7ashbco # aligned letter pairs: 14897.4 # deletes: 188.951 diff -r 3de2195f32c0 -r 8705e0d74a0f test-data/last_train_E.txt --- a/test-data/last_train_E.txt Fri Nov 13 09:05:49 2020 +0000 +++ b/test-data/last_train_E.txt Wed Mar 24 22:36:50 2021 +0000 @@ -1,9 +1,9 @@ -# lastal version: 1021 +# lastal version: 1205 # maximum percent identity: 100 # 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 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -r5 -q5 -a15 -b3 -A15 -B3 /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14901 # deletes: 694 @@ -47,7 +47,7 @@ # G -88 -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 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.4322 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14771 # deletes: 379.3 @@ -63,21 +63,21 @@ # delExtendProb: 0.511732 # insExtendProb: 0.566038 -# substitution percent identity: 70.0105 +# substitution percent identity: 70.0152 # count matrix (query letters = columns, reference letters = rows): # A C G T -# A 3158 583.4 429.9 391.6 +# A 3158 582.4 429.9 391.6 # C 589 3065 156.8 774 # G 252.2 88.64 1571 68.46 # T 342.6 630.1 131.09 2566 # 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 0.213425 0.0393599 0.0290536 0.0264652 +# C 0.0398059 0.20714 0.0105969 0.0523086 +# G 0.0170442 0.00599049 0.106172 0.00462668 +# T 0.0231537 0.0425836 0.00885935 0.173416 # delExistCost: 406 # insExistCost: 400 @@ -86,218 +86,218 @@ # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 75 -79 -48 -102 +# A 76 -79 -48 -102 # C -78 72 -140 -41 # G -79 -174 146 -185 # T -107 -52 -136 89 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8564 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.6863 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14881 -# deletes: 258.8 -# inserts: 446.1 -# delOpens: 112.91 -# insOpens: 168 +# deletes: 264.3 +# inserts: 451.9 +# delOpens: 116.18 +# insOpens: 171.3 # 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 +# mean delete size: 2.27492 +# mean insert size: 2.63806 +# matchProb: 0.980854 +# delOpenProb: 0.00765779 +# insOpenProb: 0.0112909 +# delExtendProb: 0.560424 +# insExtendProb: 0.620934 -# substitution percent identity: 68.9366 +# substitution percent identity: 68.9602 # 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 3126 617.2 445 406.6 +# C 621.9 3041 159.4 804.4 +# G 264.2 91.07 1560 68.32 +# T 357.3 658.9 133.32 2554 # 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 0.209677 0.0413989 0.0298485 0.0272728 +# C 0.0417142 0.203976 0.0106918 0.0539554 +# G 0.0177213 0.00610855 0.104638 0.00458259 +# T 0.023966 0.0441959 0.00894248 0.17131 -# delExistCost: 470 -# insExistCost: 457 +# delExistCost: 466 +# insExistCost: 453 # delExtendCost: 52 -# insExtendCost: 42 +# insExtendCost: 43 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 75 -73 -44 -99 +# A 75 -74 -44 -99 # C -73 71 -138 -37 -# G -73 -171 147 -185 +# G -74 -171 147 -185 # T -103 -48 -134 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1831 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1379 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 -# deletes: 214.8 -# inserts: 402.9 -# delOpens: 82.32 -# insOpens: 131.98 +# deletes: 217 +# inserts: 405.1 +# delOpens: 83.75 +# insOpens: 134.12 # 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 +# mean delete size: 2.59104 +# mean insert size: 3.02043 +# matchProb: 0.985471 +# delOpenProb: 0.00550919 +# insOpenProb: 0.0088226 +# delExtendProb: 0.614055 +# insExtendProb: 0.668921 -# substitution percent identity: 68.4035 +# substitution percent identity: 68.4369 # 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 3114 634.8 449.1 416.3 +# C 639 3019 163.9 815.3 +# G 269.6 93.35 1560 69.28 +# T 364.7 670 135.51 2543 # 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 0.208199 0.0424421 0.0300264 0.0278334 +# C 0.0427229 0.201847 0.0109582 0.0545102 +# G 0.0180252 0.00624129 0.1043 0.00463199 +# T 0.0243835 0.0447956 0.00906007 0.170023 -# delExistCost: 518 -# insExistCost: 498 +# delExistCost: 516 +# insExistCost: 495 # delExtendCost: 44 # insExtendCost: 36 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -71 -43 -97 +# A 75 -71 -43 -97 # C -70 71 -135 -36 -# G -71 -169 146 -183 +# G -72 -169 147 -183 # T -101 -46 -133 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.7211 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.7798 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 -# deletes: 197.5 -# inserts: 386.4 -# delOpens: 68.51 -# insOpens: 115.71 +# deletes: 204.2 +# inserts: 393.3 +# delOpens: 71.01 +# insOpens: 119.07 # 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 +# mean delete size: 2.87565 +# mean insert size: 3.3031 +# matchProb: 0.987276 +# delOpenProb: 0.00467969 +# insOpenProb: 0.00784693 +# delExtendProb: 0.652253 +# insExtendProb: 0.697254 -# substitution percent identity: 68.1501 +# substitution percent identity: 68.1926 # 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 3104 642.4 451.1 421.4 +# C 647.7 3009 167 819.4 +# G 271.7 94.39 1560 70.33 +# T 368.8 674.3 136.58 2543 # 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 0.207194 0.0428807 0.0301113 0.0281288 +# C 0.0432345 0.200853 0.0111474 0.0546956 +# G 0.0181362 0.00630061 0.104131 0.00469458 +# T 0.0246177 0.04501 0.00911682 0.169747 -# delExistCost: 549 -# insExistCost: 522 +# delExistCost: 545 +# insExistCost: 517 # delExtendCost: 39 -# insExtendCost: 32 +# insExtendCost: 33 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -43 -95 -# C -68 70 -134 -35 +# A 74 -70 -43 -96 +# C -69 70 -134 -35 # G -71 -168 146 -182 -# T -100 -45 -132 88 +# T -100 -46 -132 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 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.3541 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 -# deletes: 192.1 -# inserts: 380.9 -# delOpens: 62.34 -# insOpens: 108.21 +# deletes: 194.4 +# inserts: 382.1 +# delOpens: 63.11 +# insOpens: 109.31 # 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 +# mean delete size: 3.08034 +# mean insert size: 3.49556 +# matchProb: 0.988426 +# delOpenProb: 0.00416391 +# insOpenProb: 0.00721213 +# delExtendProb: 0.67536 +# insExtendProb: 0.713923 -# substitution percent identity: 67.9883 +# substitution percent identity: 68.0193 # 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 3093 646.9 451.1 424.6 +# C 652.9 3008 168 821.5 +# G 272.7 95.16 1550 70.95 +# T 370.8 676.5 136.64 2532 # 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 0.206603 0.0432109 0.0301321 0.028362 +# C 0.0436117 0.200925 0.0112219 0.0548737 +# G 0.0182155 0.00635639 0.103535 0.00473924 +# T 0.0247683 0.0451881 0.00912713 0.16913 -# delExistCost: 566 -# insExistCost: 534 +# delExistCost: 565 +# insExistCost: 533 # delExtendCost: 36 # insExtendCost: 30 # score matrix (query letters = columns, reference letters = rows): # A C G T -# A 74 -69 -42 -94 +# A 74 -69 -42 -95 # C -68 70 -133 -35 # G -70 -167 147 -181 # T -99 -45 -131 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 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1953 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 -# deletes: 194.5 -# inserts: 383.3 -# delOpens: 60.42 -# insOpens: 106.36 +# deletes: 195.6 +# inserts: 384.5 +# delOpens: 60.75 +# insOpens: 106.8 # 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 +# mean delete size: 3.21975 +# mean insert size: 3.60019 +# matchProb: 0.988744 +# delOpenProb: 0.00400949 +# insOpenProb: 0.00704878 +# delExtendProb: 0.689417 +# insExtendProb: 0.722237 -# substitution percent identity: 67.9593 +# substitution percent identity: 67.9748 # 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 3093 648.9 451.2 425.6 +# C 655.1 3008 169 821.4 +# G 272.8 95.36 1550 71.16 +# T 372.8 677.6 136.64 2532 # 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 0.206468 0.0433161 0.030119 0.0284102 +# C 0.04373 0.200794 0.0112813 0.0548311 +# G 0.0182103 0.00636558 0.103467 0.00475016 +# T 0.0248856 0.045232 0.00912115 0.169019 # delExistCost: 575 # insExistCost: 539 @@ -307,41 +307,41 @@ # 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 +# C -68 70 -133 -35 +# G -70 -167 147 -181 # 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 +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.1816 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 # deletes: 196.9 # inserts: 385.7 -# delOpens: 59.47 -# insOpens: 105.68 +# delOpens: 59.46 +# insOpens: 105.67 # 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 +# mean delete size: 3.31147 +# mean insert size: 3.65004 +# matchProb: 0.988902 +# delOpenProb: 0.00392498 +# insOpenProb: 0.00697532 +# delExtendProb: 0.698019 +# insExtendProb: 0.726031 -# substitution percent identity: 67.9572 +# substitution percent identity: 67.9622 # 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 +# C 655 3008 168.9 821.4 # G 273.8 95.45 1550 71.26 -# T 372.7 678.6 136.63 2532 +# T 372.7 678.6 136.62 2532 # 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 +# A 0.206429 0.0433015 0.0301135 0.0284716 +# C 0.0437152 0.200756 0.0112725 0.0548209 +# G 0.0182736 0.00637041 0.103448 0.00475595 +# T 0.0248743 0.0452903 0.00911813 0.168988 # delExistCost: 580 # insExistCost: 541 @@ -351,11 +351,11 @@ # score matrix (query letters = columns, reference letters = rows): # A C G T # A 74 -69 -42 -94 -# C -68 70 -132 -35 +# C -68 70 -133 -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 +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.131 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 # deletes: 197 @@ -371,21 +371,21 @@ # delExtendProb: 0.701929 # insExtendProb: 0.727405 -# substitution percent identity: 67.9308 +# substitution percent identity: 67.9358 # 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 +# C 656 2998 168.9 821.4 +# G 273.8 95.45 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 +# A 0.206552 0.0433272 0.0301314 0.0284886 +# C 0.043808 0.200208 0.0112792 0.0548535 +# G 0.0182845 0.0063742 0.10351 0.00476546 +# T 0.0248891 0.0453173 0.00912355 0.169088 # delExistCost: 584 # insExistCost: 542 @@ -397,9 +397,9 @@ # A 74 -69 -42 -94 # C -68 70 -132 -35 # G -70 -166 146 -180 -# T -99 -45 -132 88 +# T -99 -45 -131 88 -# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.815 -p- ref_db /tmp/tmpikDSIL/tmp/tmpDOHHwB +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t90.8423 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 # deletes: 197 @@ -415,21 +415,153 @@ # delExtendProb: 0.705736 # insExtendProb: 0.728334 -# substitution percent identity: 67.93 +# substitution percent identity: 67.9254 # 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 +# T 372.7 678.6 136.62 2532 + +# probability matrix (query letters = columns, reference letters = rows): +# A C G T +# A 0.20652 0.0433205 0.0301267 0.028551 +# C 0.0438013 0.200177 0.0113443 0.0548451 +# G 0.0182817 0.00639325 0.103494 0.00476473 +# T 0.0248853 0.0453103 0.00912215 0.169062 + +# delExistCost: 586 +# insExistCost: 543 +# delExtendCost: 32 +# insExtendCost: 29 + +# score matrix (query letters = columns, reference letters = rows): +# A C G T +# A 74 -69 -43 -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 -t90.682 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 + +# aligned letter pairs: 14981 +# deletes: 194.8 +# inserts: 383.5 +# delOpens: 57.43 +# insOpens: 103.95 +# alignments: 2 +# mean delete size: 3.39196 +# mean insert size: 3.68927 +# matchProb: 0.989147 +# delOpenProb: 0.00379192 +# insOpenProb: 0.00686348 +# delExtendProb: 0.705185 +# insExtendProb: 0.728944 + +# substitution percent identity: 67.9249 + +# count matrix (query letters = columns, reference letters = rows): +# A C G T +# A 3093 649.9 451.1 427.6 +# C 656 2998 169.9 821.4 +# G 273.8 95.75 1550 71.46 +# T 372.7 678.6 135.62 2532 # 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 0.206519 0.0433937 0.0301199 0.0285508 +# C 0.043801 0.200176 0.0113442 0.0548447 +# G 0.0182816 0.00639321 0.103493 0.00477137 +# T 0.0248851 0.04531 0.00905532 0.169061 + +# delExistCost: 587 +# insExistCost: 543 +# delExtendCost: 32 +# insExtendCost: 29 + +# score matrix (query letters = columns, reference letters = rows): +# A C G T +# A 74 -68 -42 -94 +# C -68 70 -132 -35 +# G -70 -166 147 -180 +# T -99 -45 -132 88 + +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2049 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 + +# aligned letter pairs: 14981 +# deletes: 195.9 +# inserts: 384.7 +# delOpens: 57.66 +# insOpens: 104.5 +# alignments: 2 +# mean delete size: 3.3975 +# mean insert size: 3.68134 +# matchProb: 0.989096 +# delOpenProb: 0.00380691 +# insOpenProb: 0.00689944 +# delExtendProb: 0.705666 +# insExtendProb: 0.72836 + +# substitution percent identity: 67.9195 + +# count matrix (query letters = columns, reference letters = rows): +# A C G T +# A 3093 649.9 451.2 427.6 +# C 656.1 2998 169.9 821.4 +# G 273.8 95.74 1550 71.46 +# T 373.7 678.6 135.62 2532 + +# probability matrix (query letters = columns, reference letters = rows): +# A C G T +# A 0.206503 0.0433902 0.0301241 0.0285485 +# C 0.0438042 0.20016 0.0113433 0.0548404 +# G 0.0182801 0.00639203 0.103485 0.00477099 +# T 0.0249499 0.0453064 0.0090546 0.169048 + +# delExistCost: 586 +# insExistCost: 543 +# delExtendCost: 32 +# insExtendCost: 29 + +# score matrix (query letters = columns, reference letters = rows): +# A C G T +# A 74 -68 -42 -94 +# C -68 70 -132 -35 +# G -70 -166 147 -180 +# T -99 -45 -132 88 + +# lastal -j7 -D1000000 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.2167 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 + +# 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 + +# substitution percent identity: 67.9245 + +# count matrix (query letters = columns, reference letters = rows): +# A C G T +# A 3093 649.9 451.2 427.6 +# C 656.1 2998 169.9 821.4 +# G 273.8 95.64 1550 71.46 +# T 372.7 678.6 135.62 2532 + +# probability matrix (query letters = columns, reference letters = rows): +# A C G T +# A 0.206518 0.0433934 0.0301264 0.0285506 +# C 0.0438074 0.200175 0.0113441 0.0548444 +# G 0.0182815 0.00638583 0.103493 0.00477134 +# T 0.024885 0.0453097 0.00905527 0.16906 # delExistCost: 586 # insExistCost: 543 @@ -443,7 +575,7 @@ # G -70 -166 147 -180 # T -99 -45 -132 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 -E10 -s1 -S1 -T0 -m10 -k1 -P1 -X0 -Q0 -t91.0834 -p- /home/berntm/.planemo/planemo_tmp_y1t9frxe/test-data/humdb /tmp/tmpw04gddt3 # aligned letter pairs: 14981 # deletes: 196