MakeReferenceAlignment.bf throws an error when branchswapping is selected

[sdwfrost]

Using current HYPHYMP from hyphyqt branch, MakeReferenceAlignment works when there is no branch swapping, but breaks when there is. Using the AG.fas data in the Sample subdirectory, I get the following. I don't get to enter the model when it breaks.

   /HYPHY 2.220130716beta(MP) for Linux on x86_64\       

***************** TYPES OF STANDARD ANALYSES *****************

(1) Basic Analyses
(2) Codon Selection Analyses
(3) Compartmentalization
(4) Data File Tools
(5) Miscellaneous
(6) Model Comparison
(7) Kernel Analysis Tools
(8) Molecular Clock
(9) Phylogeny Reconstruction
(10) Positive Selection
(11) Recombination
(12) Selection/Recombination
(13) Relative Rate
(14) Relative Ratio
(15) Substitution Rates

Please select type of analyses you want to list (or press ENTER to process custom batch file):

/usr/local/lib/hyphy/Batch file to run::/home/simon/Dropbox/hyphy/tests/SCUEAL/TopLevel/MakeReferenceAlignment.bf

        +---------------------+
        |Codons or Nucleotides|
        +---------------------+


(1):[Codon] In-frame (universal code) codon alignment
(2):[Nucleotide] Nucleotide alignment

Please choose an option (or press q to cancel selection):1

/home/simon/Dropbox/hyphy/tests/SCUEAL/TopLevel/Reference sequences?:/home/simon/Dropbox/hyphy/tests/SCUEAL/Sample/AG.fas

        +--------------------+
        |Align the sequences?|
        +--------------------+


(1):[Yes] Align reference sequences
(2):[No] Assume that sequences are already aligned

Please choose an option (or press q to cancel selection):2

Data Read:
9 species:{A1_KE_94_Q23_17_ACC_AF004885,A1_SE_94_SE7253_ACC_AF069670,A1_UG_98_98UG57136_ACC_AF484509,A2_CD_97_97CDKTB48_ACC_AF286238,A2_CY_94_94CY017_41_ACC_AF286237,G_BE_96_DRCBL_ACC_AF084936,G_KE_93_HH8793_12_1_ACC_AF061641,G_NG_92_92NG083_ACC_U88826,G_SE_93_SE6165_ACC_AF061642};
Total Sites:3012;
Distinct Sites:349

No stop codons found

[PHASE 3]. Making a TN93 NJ tree

--------------------- INFERRED TREE ---------------------

((((((A1_KE_94_Q23_17_ACC_AF004885:0.02735907221595164,A1_SE_94_SE7253_ACC_AF069670:0.02522247938998138):0.0008897412107701438,A1_UG_98_98UG57136_ACC_AF484509:0.03644179383861834):0.02029989056635367,(A2_CD_97_97CDKTB48_ACC_AF286238:0.02885372228441906,A2_CY_94_94CY017_41_ACC_AF286237:0.0295210031169931):0.02256936849585516):0.03720743108852486,G_KE_93_HH8793_12_1_ACC_AF061641:0.02932539262632659):0.003493345310067533,G_BE_96_DRCBL_ACC_AF084936:0.02922518610527121):0.001577854135266798,G_NG_92_92NG083_ACC_U88826:0.02729191223314001,G_SE_93_SE6165_ACC_AF061642:0.02250909897834102)

***********Save this tree to a file (y/n)?

        +---------------+
        |Branch Swapping|
        +---------------+


(1):[Yes] Do branch swapping
(2):[No] Skip branch swapping

Please choose an option (or press q to cancel selection):1

[PHASE 4]. Doing Branch Swapping
urrent Max: -9312.4816 (96 % done) LF Evals/Sec: 5352 CPU Load: 2.796 �

****** ORIGINAL TREE AND LIKELIHOOD ******

Log Likelihood = -9312.48163836232;
Shared Parameters:
c_scale=RS_1_PS_1+1_(1-PS_1)PS_2+1_RS_3(1-PS_1)_(1-PS_2)=3.808340324903829
PS_2=0.6640290759788783=0.6640290759788783
PS_1=0.4194091350944347=0.4194091350944347
RS_1=1=1
RS_3=15.3971935750066=15.3971935750066
GT=0.1063956748896619=0.1063956748896619
AT=0.08623335219617401=0.08623335219617401
AC=0.2776834603845991=0.2776834603845991
CG=0.1135709799592191=0.1135709799592191
CT=1.565657248315703=1.565657248315703

Tree givenTree=(((G_NG_92_92NG083_ACC_U88826:0.02963935030928721,G_SE_93_SE6165_ACC_AF061642:0.0260543552886263)intNode3:0.002292081728264686,G_BE_96_DRCBL_ACC_AF084936:0.03502289061206555)intNode2:0.005743281166408801,G_KE_93_HH8793_12_1_ACC_AF061641:0.03172111289251599,(((A1_KE_94_Q23_17_ACC_AF004885:0.0316834824535026,A1_SE_94_SE7253_ACC_AF069670:0.02637312555354242)intNode10:0.004178853474606632,A1_UG_98_98UG57136_ACC_AF484509:0.04296626315404546)intNode9:0.03130935338136338,(A2_CD_97_97CDKTB48_ACC_AF286238:0.03447160365399183,A2_CY_94_94CY017_41_ACC_AF286237:0.0329741660838478)intNode14:0.03380323680007909)intNode8:0.06041971729901392);

****** RUNNING BRANCH SWAPPING ANALYSIS ******

PHASE 1

0). Swap at:intNode3.Log-L = -9314.22922 ( -1.74758)
1). Swap at:intNode3.Log-L = -9314.67858 ( -2.19695)
2). Swap at:intNode2.Log-L = -9307.97855 ( 4.50309)

**** AFTER PHASE 1

Best Tree:
(((G_KE_93_HH8793_12_1_ACC_AF061641:0.02932539262632659,(G_NG_92_92NG083_ACC_U88826:0.02729191223314001,G_SE_93_SE6165_ACC_AF061642:0.02250909897834102)intNode3:0.001577854135266798),G_BE_96_DRCBL_ACC_AF084936:0.02922518610527121):0.03720743108852486,(((A1_KE_94_Q23_17_ACC_AF004885:0.02735907221595164,A1_SE_94_SE7253_ACC_AF069670:0.02522247938998138)intNode10:0.0008897412107701438,A1_UG_98_98UG57136_ACC_AF484509:0.03644179383861834)intNode9:0.02029989056635367,(A2_CD_97_97CDKTB48_ACC_AF286238:0.02885372228441906,A2_CY_94_94CY017_41_ACC_AF286237:0.0295210031169931)intNode14:0.02256936849585516)intNode8:0.03720743108852486)
Log-likelihood = -9315.723670566054 (Improvement of -3.242032203734198)

PHASE 2

3). Swap at:intNode3.Log-L = -9748.57480 (-436.09316)
4). Swap at:intNode3.Log-L = -9760.79343 (-448.31179)
5). Swap at:Node2.Log-L = -9751.16500 (-438.68336)
6). Swap at:Node2.Log-L = -9751.16500 (-438.68336)
7). Swap at:intNode10.Log-L = -9664.63015 (-352.14851)
8). Swap at:intNode10.Log-L = -9595.22557 (-282.74393)
9). Swap at:intNode9.Log-L = -9745.33395 (-432.85231)
10). Swap at:intNode9.Log-L = -9748.19232 (-435.71069)
11). Swap at:intNode14.Log-L = -9764.85251 (-452.37087)
12). Swap at:intNode14.Log-L = -9728.95746 (-416.47583)
13). Swap at:intNode8.Log-L = -10071.97278 (-759.49114)
14). Swap at:intNode8.Log-L = -10032.52199 (-720.04035)

***** 15 TREE REARRANGEMENTS WERE EXPOLORED *****

***** RELATIVE TREE SUPPORT (WITH UN-INFORMATIVE PRIOR): 0.02951054972485281 ******

***** BRANCH SWAPPING FOUND A BETTER TREE! *****

((G_KE_93_HH8793_12_1_ACC_AF061641,(G_NG_92_92NG083_ACC_U88826,G_SE_93_SE6165_ACC_AF061642)),G_BE_96_DRCBL_ACC_AF084936,(((A1_KE_94_Q23_17_ACC_AF004885,A1_SE_94_SE7253_ACC_AF069670),A1_UG_98_98UG57136_ACC_AF484509),(A2_CD_97_97CDKTB48_ACC_AF286238,A2_CY_94_94CY017_41_ACC_AF286237)));

A likelihood improvement of -3.242032203734198

[PHASE 5]. Fitting a model to estimate the ancestor
READ THE FOLLOWING DATA
9 species:{A1_KE_94_Q23_17_ACC_AF004885,A1_SE_94_SE7253_ACC_AF069670,A1_UG_98_98UG57136_ACC_AF484509,A2_CD_97_97CDKTB48_ACC_AF286238,A2_CY_94_94CY017_41_ACC_AF286237,G_BE_96_DRCBL_ACC_AF084936,G_KE_93_HH8793_12_1_ACC_AF061641,G_NG_92_92NG083_ACC_U88826,G_SE_93_SE6165_ACC_AF061642};
Total Sites:3012;
Distinct Sites:349
Please enter a 6 character model designation (e.g:010010 defines HKY85):Error:
Cannot reuse the filter 'filteredData' because it is already being used by likelihood function 'theLF', and the two likelihood functions impose different leaf-to-sequence mapping. Create a copy the filter and pass it to the second likelihood function to resolve this issue.

Function call stack
1 : Construct the following likelihood function:filteredData ; givenTree ;
Standard input redirect:
Empty Associative List-------
2 : ExecuteAFile from file HYPHY_BASE_DIRECTORY+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"AnalyzeCodonData.bf" using basepath /home/simon/Dropbox/hyphy/tests/SCUEAL/TopLevel/. reading input from codonOptions
{"0":"Universal",
"1":"/home/simon/Dropbox/hyphy/tests/SCUEAL/Sample/AG.fas",
"2":"MG94CUSTOM",
"3":"Global",
"4":"012345",
"6":"/home/simon/Dropbox/hyphy/tests/SCUEAL/Sample/AG_nj.tree",
"7":"Estimate"}