Hello, it can be stupid but I have a question interpreting a result file of Phylonet MCMC_BiMarkers result file.
I made an input file from vcf file to next file. The data of input file is like:
#NEXUS
Begin data;
Dimensions ntax=7 nchar=91507;
Format datatype=dna symbols="012" missing=? gap=-;
Matrix
CNGR_1 02000002...
CNHR_1 11201000...
CNMK_1 10001200...
CNTJ_5 00022210...
CNYS_BH_1 20102...
CTSJ_10 2210220...
Ilongicorpa 000...
;End;
BEGIN PHYLONET;
MCMC_BiMarkers -cl 500000 -bl 200000 -sf 500 -diploid -varytheta -mr 10 -pl 50 -sd 12345678 -taxa (CNGR_1,CNHR_1,CNMK_1,CNTJ_5,CNYS_BH_1,CTSJ_10,Ilongicorpa) -tm <Cnalbanti_GR:CNGR_1;Cnalbanti_HR:CNHR_1;Cnalbanti_MK:CNMK_1;Cnalbanti_TJ:CNTJ_5;Cnalbanti_YS_BH:CNYS_BH_1;Ctetralineata:CTSJ_10;Ilongicorpa:Ilongicorpa>;
END;
I ran the program with the command
java -Xmx400g -Xms200g -jar /path/to/apps/phylonet/Phylonet.jar /path/to/input/file/binary_data_gapfree.nex > ./result_gapfree.txt
because when using MLE_BiMarkers, my server CPU was almost overloaded, so I stopped it while running.
I started MCMC_BiMarkers on January 3rd, but till now it didn't stop. It is still at iteration 63. My supervisor did the same job with similar taxa (same family / 1 individual for each taxon / total 8 taxa / nchar=81000 / same options) in same server, and it took only a few days. The difference in command is a java heap memory option. She didn't put heap memory options. I don't think that this affects that much in running speed of analysis but I want to know the reason why it takes so long.
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Another question is about the result file. It didn't finish but this is the part of the file.
----------------------- Logger: -----------------------
Iteration; Posterior; ESS; Likelihood; Prior; ESS; #Reticulation
0; -645900.05505; 0.00000; -645938.30933; 38.25428; 0.00000; 0;
[0.036](((((Cnalbanti_GR:0.18704589107487574:0.036,Cnalbanti_HR:0.18704589107487574:0.036):0.02309687693853249:0.036,Cnalbanti_MK:0.21014276801340823:0.036):0.09426957916426001:0.036,Cnalbanti_YS_BH:0.30441234717766824:0.036):0.37246265282233165:0.036,Ctetralineata:0.6768749999999999:0.036):0.03562500000000002:0.036,(Ilongicorpa:0.6768749999999999:0.036,Cnalbanti_TJ:0.6768749999999999:0.036):0.03562500000000002:0.036);
Topology: ((Cnalbanti_TJ,Ilongicorpa),(Ctetralineata,(Cnalbanti_YS_BH,(Cnalbanti_MK,(Cnalbanti_HR,Cnalbanti_GR)))));
Gamma Mean: 0.018
Temperature = 1.0 (main)
1; -574980.80000; 0.00000; -575008.82805; 28.02805; 0.00000; 0;
[0.08353380074890372](Ilongicorpa:0.8829604363522213:0.056761423814149004,(Cnalbanti_TJ:0.6483314136520049:0.057843379389168115,((((Cnalbanti_MK:0.023080764184798076:0.06221153214118039,Cnalbanti_YS_BH:0.023080764184798076:0.060792837933153994)I3:0.02145402335618913:0.056761423814149004,Cnalbanti_HR:0.044534787540987206:0.056761423814149004)I4:0.005333284285660447:0.056761423814149004,Cnalbanti_GR:0.04986807182664765:0.056761423814149004)I5:0.3815185496830193:0.04545036971559996,Ctetralineata:0.43138662150966695:0.0768836095963774)I2:0.21694479214233792:0.04647889915746812)I1:0.23462902270021646:0.04580328645628045)I0;
(···)
Temperature = 1.0 (main)
63; -509463.45000; 0.00000; -509425.26400; -38.18600; 0.00000; 2;
[0.01426491357264947](((((Cnalbanti_YS_BH:0.007228067465656309:0.46400931892705044,(Cnalbanti_MK:0.0014032278336445628:0.30323081185941547,(Cnalbanti_GR:0.0011872239682340269:0.011635588907393489,Cnalbanti_HR:0.0011872239682340269:0.00789675182216521)I4:2.1600386541053597E-4:0.006880141544908149)I3:0.005824839632011746:0.03941434326294445)I5:0.12960323386272166:0.23344121872616386)I9#H1:0.0010007781448575226:0.06235999959471413:0.4221282282944794,Ctetralineata:0.13783207947323547:0.28880882452892204)I2:0.17757699748172426:0.03441989631070512,(Cnalbanti_TJ:0.006057889343246891:0.13224807135548988)I7#H2:0.3093511876117128:0.23412740310411062:0.746797894317327)I1:4.082052241654127:0.19208730881560857,(I9#H1:0.37245373164718043:0.1450520372416931:0.5778717717055206,(I7#H2:0.242984927714842:0.014528141466961946:0.25320210568267304,Ilongicorpa:0.2490428170580889:0.044603518098365665)I6:0.2602422159174695:0.002155280646248993)I0:3.888176285633528:0.02300914550784399)I8;
Topology: (((Ilongicorpa,(Cnalbanti_TJ)I7#H1)I6,((((Cnalbanti_HR,Cnalbanti_GR)I4,Cnalbanti_MK)I3,Cnalbanti_YS_BH)I5)I9#H2)I0,(I7#H1,(Ctetralineata,I9#H2)I2)I1)I8;
Gamma Mean: 0.018
Super long: (((((Cnalbanti_MK:0.0014032278336445628:0.3102155401113268,((Cnalbanti_GR:7.419064867077346E-4:0.011635588907393489)#H2:4.4531748152629223E-4:0.011858736223304849:0.10777464043877871,Cnalbanti_HR:0.0011872239682340269:0.00789675182216521)I4:2.1600386541053597E-4:0.006880141544908149)I3:0.005824839632011746:0.03941434326294445,Cnalbanti_YS_BH:0.007228067465656309:0.46400931892705044)I5:0.12960323386272166:0.23344121872616386)I9#H1:0.37245373164718043:0.1450520372416931:0.5778717717055206,(Ilongicorpa:0.2490428170580889:0.044603518098365665,(Cnalbanti_TJ:0.006057889343246891:0.13224807135548988)I7#H3:0.242984927714842:0.014528141466961946:0.253202105682673)I6:0.2602422159174695:0.002155280646248993)I0:5.094944572546711:0.009117773023899989,(I7#H3:0.3093511876117128:0.23412740310411062:0.746797894317327,((#H2:0.1370694831549978:0.021082429592139365:0.8922253595612213,I9#H1:9.80088313327604E-4:0.04284268552137498:0.4221282282944794):2.0689831529918656E-5:0.05487584292361063,Ctetralineata:0
(···)
Until iteration 52, there was no "Super long". "Super long" is different from the topology of each iteration. From iteration 53, multiple "Super long" was printed in the result txt file. The number of Super long for each iteration was different and all Super long in each iteration were made up of the same value. I don't know what this Super long means.
