kr-colab/discoal

discoal is a coalescent simulation program capable of simulating models with recombination, selective sweeps, and demographic changes including population splits, admixture events, and ancient samples

discoal's Issues

How to deal with different races

I am wondering how to differentiate/simulate different races, say Japanese, European, American, Chinese, during discoal process?

Errors when using deterministic sweeps (-wd)

Hi,

discoal is producing errors relating to population size changes when using the -wd command (deterministic sweeps), even though no population size changes are being defined.

Example command:
discoal 30 1 100000 -t 50 -r 50 -wd 0 -a 500 -x 0.5

Error produced:
"Error with event specification: you chose 1 or more population size changes with a determinstic sweep. Please us -ws flag instead". (There also seems to be a typo in 'deterministic'.)

Thanks for looking into this!

Selection start and multiple populations

Hi @andrewkern,
I have a question about how to simulate selection after a population split. Namely, I want to train a model where selection can only start after a population split. My thought is that if I use commands like -p 2 2 2 and -ed 0.5 0 1 -ws 0 ... selection stops at time 0 (sampling time) and can only start after the split time going forward since the population under selection (here id 0) doesnt exist until after that time. Am I on the right track?
thanks,
@stsmall

documentation fix

All times are in units of 4N generations. Need to fix the documentation to reflect this.

Questions in scaled parameter settings

Dear Andrew,

I was trying to use discoal to simulate data to feed diploS/HIC, I have read the manual carefully and also the Kern and Schrider 2018 paper. However, I still not sure about the setting of population parameters. The manual mentioned the mutation rate u, recombination rate p, and selection coefficient s are scaled by 4N0 where N0 is the most recent (current) effective population size. However, I could not find a clear statement of the units of u, p, and s themselves - are they in the units of per generation per length of the simulated locus instead of per generation per bp?

In the Table S1 of the Kern and Schrider 2018 paper, the mutation rate and recombination rate were scaled by 4NL and 4NrL, respectively, where L is the length of the simulated chromosome. However, the selection coefficient was scaled by 2Ns, where the unit of s is not given. These seem to be not consistent with the manual. Could you please clarify these three parameters?

For the simulation of the mosquito case, a very short time of selection were simulated with 4N0T = 0.000040 where T is the generation backward from the present. Is it set for the purpose of capturing the recent soft sweep of the Gste locus? Does diploS/HIC have power to detect ancient sweeps (eg. 10,000 generations ago) given the corresponding training set?

The time setting for demographic changes is also not clear to me. From the manual, I learn that -en specify the time in unit of 4N0, so if I have N0 = 2500, then -en 0.5 0 0.1 means at generation 5000 (4*2500*0.5), pop 0 has a shrinkage of Ne to 10%? Does this time count backward from the present or forward from some point? If it's backward, then the example given in the manual -en 0.5 0 0.1 -en 1.2 0 0.8 should be explained as the population has a shrinkage to 80% in the time of 1.2 (older) and further shrunk to 10% in the time of 0.5 (closer to the present), but not as in the manual "at time 0.5 the population crashes to 10% of its initial size and then at time 1.2 it rebounds to 80% of its initial size.". Please help to clarify.

Thank you very much in advance!

Shujun

Tree output mode with recombination

when I simulate in tree mode with vs. without recombination, I get very different trees at the selected site: (simulating partial sweep with 1 ancient sample)

(1) no recom (rho=0)
$ ./discoal 51 1 100000 -t 0 -r 0 -A 1 0 0.5 -x 0.5 -c 50e-2 -ws 0 -a 200 -N 10000

(2) with recom (rho=1)
$ ./discoal 51 1 100000 -t 0 -r 1 -A 1 0 0.5 -x 0.5 -c 50e-2 -ws 0 -a 200 -N 10000
The trees without recom (1) look normal. But (2) produces local trees that have very long terminal branches; e.g.

(((14:1.426351,(3:1.417362,7:1.417362):0.008989):0.001227,(((42:0.770007,(2:0.718529,(21:0.701219,8:0.701219):0.017310):0.051478):0.041590,(((22:0.721283,46:0.721283):0.030267,(((49:0.715397,(36:0.702613,(12:0.700720,30:0.700720):0.001893):0.012785):0.003924,(9:0.711552,(16:0.709964,(18:0.705181,11:0.705181):0.004783):0.001588):0.007770):0.013743,(40:0.719578,44:0.719578):0.013486):0.018486):0.010561,((48:0.708968,19:0.708968):0.033373,24:0.742341):0.019770):0.049486):0.057823,(((20:0.803319,29:0.803319):0.003727,26:0.807046):0.021534,6:0.828580):0.040839):0.558159):0.073415,(0:0.627141,((27:0.667150,((13:0.563922,(33:0.559686,43:0.559686):0.004236):0.018902,(((((39:0.551358,28:0.551358):0.005595,(32:0.553924,(17:0.549684,4:0.549684):0.004241):0.003029):0.009503,(5:0.558221,38:0.558221):0.008236):0.000828,31:0.567285):0.003854,((37:0.547439,(45:0.546483,23:0.546483):0.000957):0.007550,(35:0.551138,(50:0.550607,(41:0.544904,1:0.544904):0.005703):0.000532):0.003851):0.016149):0.011686):0.084326):0.123691,((10:0.547810,15:0.547810):0.053473,((34:0.546782,47:0.546782):0.031666,25:0.578448):0.022836):0.189558):0.336300):0.373851);

which looks like this when i plot it in Dendroscope:

rho is per-base or for the whole locus?

Dear Prof. Kern, could you clarify whether in discoal the rho parameter is per-base or should I multiply it by the length of the locus?

Rongfeng Cui
Thank you!

Multiple Population with selection

Hi @andrewkern,
Sorry for what is likely a lazy question. I would like to simulate 2 populations with discoal with 1 population under selection. Does discoal allow this? If not, what is the behavior with >1 populations and selection? Are both populations under selection? This command runs, I just want to verify that I understand it. I assume that both populations are under selection starting at time designated by option Pu.
'discoal 12 1000 55000 -Pt 154 698 -Pr 344 1556 -ed 2 12 0 -ws 0 -Pa 450 4500 -Pu 0.000000 0.00045 -x 0.045454545454545456 -ed 1 0 1'
thanks,
@stsmall

Code is using feature removed in Python 3.3

Running the example gives:

AttributeError: module 'time' has no attribute 'clock'

The reason is that clock was deprecated, and eventually removed.

Error: `currentTrajectory' failed

When I run the command, the script often runs for a while and then ends with the following error
discoal_multipop.c:57: main: Assertion `currentTrajectory' failed
especially when there are many -en parameters. Could you tell me why am I getting this error? I generated the script using the generateSimLaunchScript.py tool in diploSHIC package.

Generation per year parameter in generateSimLaunchScript.py

Hi,

I was using generateSimLaunchScript.py to generate a bash script. I am using it to generate simulations for gorilla dataset I have. Gorillas have a generation time of 19 years. In your generateSimLaunchScript.py you have a variable gensPerYear. Does this variable have to be integer? Because I write 1.0/19.0 since generation time is 19 years. However, when I run the bash script I get the following error:

discoal: discoalFunctions.c:2067: makeGametesMS: Assertion `size < 40000' failed.
launch_script.sh: line 5: 49509 Aborted (core dumped) ./discoal 30 2000 100000 -Pt 3876.000000 38760.000000 -Pre 66.300000 198.900000 > /home/noor/Simulation/training/Neut.msOut

Could you clarify why I'm getting this error.

gcc 10 compilation error: multiple definition

1. With gcc 10 on my debian sid , make can not compile successfully!

make

gcc -O2   -o discoal discoal_multipop.c discoalFunctions.c ranlibComplete.c alleleTraj.c -lm
/usr/bin/ld: /tmp/ccwFmeUS.o:(.bss+0x40d1e4): multiple definition of `npops'; /tmp/ccnerq3Q.o:(.bss+0x40d204): first defined here
..
/usr/bin/ld: /tmp/ccwFmeUS.o:(.bss+0x40d1fc): multiple definition of `sampleNumber'; /tmp/ccnerq3Q.o:(.bss+0x40d21c): first defined here
collect2: error: ld returned 1 exit status
make: *** [Makefile:12: discoal] Error 1

2. It seems gcc 10 use -fno-common by default. Adding -fcommon flag makes it work again.

gcc -O2   -o discoal discoal_multipop.c discoalFunctions.c ranlibComplete.c alleleTraj.c -lm -fcommon

fixed this.

Printing trajectory + trees + ms

Hi Andy,

My friend (@ammodramus on github) forked discoal to try to help me hack a way to print the ms, trees, and trajectory all together (see https://github.com/ammodramus/discoal). This modification appears to print the trajectories correctly.

Problem is, the tree printing seems to work funky in the ammodramus fork. Our modification was just taking the printTreeAtSite() call outside of the -T mode if-statement, so trees are always printed. This does print out the local trees, but the branch lengths look very odd; when rho is large (say, 100) the local trees have extremely long terminal branches. See e.g. this shitty visualization of a local tree generated by './discoal 51 1 100000 -t 0 -r 10 -A 1 0 0.5 -x 0.5 -c 50e-2 -ws 0 -a 200 -N 10000':

but oddly, when we set rho=0 the trees do not have this distorted quality: e.g. './discoal 51 1 100000 -t 0 -r 0 -A 1 0 0.5 -x 0.5 -c 50e-2 -ws 0 -a 200 -N 10000'

Do you have any idea why this is so we can fix the bug?

Thanks,
Aaron

sample size issue: need recompile

I just ran discoal with sample size 500. An error message showed that I need to recompile discoal with flag -DBIG. Could you advise me how to recompile discoal? Thanks.

trajectory too bigly

Hello, When i used the discoal, i used the question as follows:
i also change the discoal.h, I can increase the define on line 119 to a larger number.But i still have the same question.

trajectory too bigly. step= 50000000000 freq = 1.000000. killing myself gently

this is our code:
/public/home/pengyan/biosoft/discoal/discoal 18 1000 1100000 -Pt 11.057476220207999 49.14433875648 -Pr 6.450194461787999 40.236927356868 -ws 0 -Pa 739.957373322 991.263651054 -Pu 0 0.05 -Pf 0 0.2 -x 0.045454545454545456-en 0.0005123594455420342 0 1.0 -en 0.0006049945447130395 0 0.9999759043822755 -en 0.0007143781617403659 0 1.0001175973010572 -en 0.0008435384455698648 0 1.0029344631843478 -en 0.0009960510380363108 0 1.0133665133649477 -en 0.0011761380592139644 0 1.0387192901658302 -en 0.0013887849934739569 0 1.0858933719555524 -en 0.001639878705137193 0 1.1629591568885242 -en 0.001936370411402724 0 1.2882524614416981 -en 0.002286468113513557 0 1.48797233867264 -en 0.0026998638280081627 0 1.7695179130949956 -en 0.0031880019010682437 0 2.12247787175784 -en 0.003764395824957696 0 2.5250306571199475 -en 0.004445002343599473 0 2.970739432288111 -en 0.005248663201508407 0 3.4574194687113566 -en 0.006197626743972406 0 3.9814785202741185 -en 0.007318163839748038 0 4.537918146940054 -en 0.008641295161738328 0 5.120402501254934 -en 0.010203649945325195 0 5.721394463107419 -en 0.012048480032755063 0 6.332354421233643 -en 0.014226857239327694 0 6.943992688081553 -en 0.016799087224164594 0 7.546562939038391 -en 0.019836378938834744 0 8.130181295108308 -en 0.02342281603437426 0 8.685154228449564 -en 0.0276576845462343 0 9.202298112052004 -en 0.03265822149796196 0 9.673234260516272 -en 0.03856286050734812 0 10.090645320147127 -en 0.045535064150699 0 10.448481816121573 -en 0.05376784916296355 0 10.742111116853538 -en 0.06348912991905076 0 10.968404899059198 -en 0.07496802794592912 0 11.125764867130398 -en 0.08852232216070617 0 11.214089951407326 -en 0.10452724630306809 0 11.234691036293558 -en 0.12342587668851686 0 11.190161556883046 -en 0.1457413982752102 0 11.084213702335639 -en 0.17209158853612302 0 10.921490681927809 -en 0.20320591926660578 0 10.707365544085508 -en 0.23994575225178202 0 10.44773637115422 -en 0.28332818356385014 0 10.148826605437552 -en 0.3345542016489557 0 9.816997852441057 -en 0.39504193499643186 0 9.458580861298259 -en 0.46646591092727446 0 9.079728710610912 -en 0.5508034127806999 0 8.686294632113915 -en 0.650389219175433 0 8.283735376081774 -en 0.7679802387977698 0 7.877039800458334 -en 0.906831831933108 0 7.47068130992789 -en 1.0707879315572497 0 7.068591977532621 -en 1.2643874575662444 0 6.674155707278724 -en 1.4929899715442896 0 6.290217442342519 -en 1.7629240467779466 0 5.919105364754637 -en 2.0816624724269146 0 5.562663082578437 -en 2.458029123724286 0 5.234511473696049 -en 2.9024432420182307 0 5.506560850643605 -en 3.427207874522306 0 6.3459278355979185 -en 4.046850476232654 0 7.22699384954018 -en 4.77852507847275 0 7.935169380554136 -en 5.642487179059596 0 8.304416097339134 -en 6.662654488820973 0 8.293892528792151 -en 7.867269065790819 0 8.007797749589406 -en 9.289679158948962 0 7.625175385724137 -en 10.969262416833702 0 7.280676891769579 -en 12.952516002768839 0 7.00133644204606 -en 15.294343809822708 0 6.706180402692751 -en 18.059576425066336 0 6.360982768384097 -en 21.32476585449663 0 5.99743151473244 -en 25.1803047942492 0 5.657142438742077 -en 29.73292901647457 0 5.395809736221858 -en 35.10867224657684 0 5.262542308833054 -en 41.45635519662705 0 5.292219047780075 -en 48.95170556431167 0 5.485757659385585 -en 57.80222276775352 0 5.8495725717114215 -en 68.2529222874877 0 6.4037220052107 -en 80.59311871070311 0 7.182799474054486 -en 95.16443496530583 0 8.238346651283726 -en 112.37025971199664 0 9.642808531127395 -en 132.68691474376973 0 11.495193845657576 -en 156.67684122873123 0 13.928695452697328 -en 185.00417043135357 0 17.120564780273064 -en 218.45310902477905 0 21.304499979541323 -en 257.949648998146 0 26.785658733040314 -en 304.58720279813053 0 33.958082369517115 -en 359.65687279960446 0 43.323739641756035 -en 424.68319412941645 0 55.51147712305491 -en 501.46633927861114 0 71.29282274080903 -en 592.1319535785387 0 91.58980409930733 -en 699.190001339254 0 117.46780571666169 -en 825.6042509899493 0 150.1042891583789 -en 974.8743229457496 0 190.7225217155683 -en 1151.1325728858374 0 240.479247750621 -en 1359.2584901053735 0 300.2977569564728 -en 1605.013780953549 0 370.64448651510696 -en 1895.2018727837517 0 451.25921707748773 -en 2237.856261592261 0 540.866179335767 -en 2642.4629066695265 0 636.9141207474848 -en 3120.2228358028515 0 735.4130877903922 -en 3684.3622360576646 0 830.9470871025904 -en 4350.498603166347 0 916.936026141531 -en 5137.073090297949 0 986.1897121260888 -en 6065.861027736246 0 1031.7388324716105 -en 7162.574752388678 0 1047.84990137343 |gzip>HN.soft_0.msOut.gz
/public/home/pengyan/biosoft/discoal/discoal 18 1000 1100000 -Pt 11.057476220207999 49.14433875648 -Pr 6.450194461787999 40.236927356868 -ws 0 -Pa 739.957373322 991.263651054 -Pu 0 0.05 -x 0.045454545454545456-en 0.0005123594455420342 0 1.0 -en 0.0006049945447130395 0 0.9999759043822755 -en 0.0007143781617403659 0 1.0001175973010572 -en 0.0008435384455698648 0 1.0029344631843478 -en 0.0009960510380363108 0 1.0133665133649477 -en 0.0011761380592139644 0 1.0387192901658302 -en 0.0013887849934739569 0 1.0858933719555524 -en 0.001639878705137193 0 1.1629591568885242 -en 0.001936370411402724 0 1.2882524614416981 -en 0.002286468113513557 0 1.48797233867264 -en 0.0026998638280081627 0 1.7695179130949956 -en 0.0031880019010682437 0 2.12247787175784 -en 0.003764395824957696 0 2.5250306571199475 -en 0.004445002343599473 0 2.970739432288111 -en 0.005248663201508407 0 3.4574194687113566 -en 0.006197626743972406 0 3.9814785202741185 -en 0.007318163839748038 0 4.537918146940054 -en 0.008641295161738328 0 5.120402501254934 -en 0.010203649945325195 0 5.721394463107419 -en 0.012048480032755063 0 6.332354421233643 -en 0.014226857239327694 0 6.943992688081553 -en 0.016799087224164594 0 7.546562939038391 -en 0.019836378938834744 0 8.130181295108308 -en 0.02342281603437426 0 8.685154228449564 -en 0.0276576845462343 0 9.202298112052004 -en 0.03265822149796196 0 9.673234260516272 -en 0.03856286050734812 0 10.090645320147127 -en 0.045535064150699 0 10.448481816121573 -en 0.05376784916296355 0 10.742111116853538 -en 0.06348912991905076 0 10.968404899059198 -en 0.07496802794592912 0 11.125764867130398 -en 0.08852232216070617 0 11.214089951407326 -en 0.10452724630306809 0 11.234691036293558 -en 0.12342587668851686 0 11.190161556883046 -en 0.1457413982752102 0 11.084213702335639 -en 0.17209158853612302 0 10.921490681927809 -en 0.20320591926660578 0 10.707365544085508 -en 0.23994575225178202 0 10.44773637115422 -en 0.28332818356385014 0 10.148826605437552 -en 0.3345542016489557 0 9.816997852441057 -en 0.39504193499643186 0 9.458580861298259 -en 0.46646591092727446 0 9.079728710610912 -en 0.5508034127806999 0 8.686294632113915 -en 0.650389219175433 0 8.283735376081774 -en 0.7679802387977698 0 7.877039800458334 -en 0.906831831933108 0 7.47068130992789 -en 1.0707879315572497 0 7.068591977532621 -en 1.2643874575662444 0 6.674155707278724 -en 1.4929899715442896 0 6.290217442342519 -en 1.7629240467779466 0 5.919105364754637 -en 2.0816624724269146 0 5.562663082578437 -en 2.458029123724286 0 5.234511473696049 -en 2.9024432420182307 0 5.506560850643605 -en 3.427207874522306 0 6.3459278355979185 -en 4.046850476232654 0 7.22699384954018 -en 4.77852507847275 0 7.935169380554136 -en 5.642487179059596 0 8.304416097339134 -en 6.662654488820973 0 8.293892528792151 -en 7.867269065790819 0 8.007797749589406 -en 9.289679158948962 0 7.625175385724137 -en 10.969262416833702 0 7.280676891769579 -en 12.952516002768839 0 7.00133644204606 -en 15.294343809822708 0 6.706180402692751 -en 18.059576425066336 0 6.360982768384097 -en 21.32476585449663 0 5.99743151473244 -en 25.1803047942492 0 5.657142438742077 -en 29.73292901647457 0 5.395809736221858 -en 35.10867224657684 0 5.262542308833054 -en 41.45635519662705 0 5.292219047780075 -en 48.95170556431167 0 5.485757659385585 -en 57.80222276775352 0 5.8495725717114215 -en 68.2529222874877 0 6.4037220052107 -en 80.59311871070311 0 7.182799474054486 -en 95.16443496530583 0 8.238346651283726 -en 112.37025971199664 0 9.642808531127395 -en 132.68691474376973 0 11.495193845657576 -en 156.67684122873123 0 13.928695452697328 -en 185.00417043135357 0 17.120564780273064 -en 218.45310902477905 0 21.304499979541323 -en 257.949648998146 0 26.785658733040314 -en 304.58720279813053 0 33.958082369517115 -en 359.65687279960446 0 43.323739641756035 -en 424.68319412941645 0 55.51147712305491 -en 501.46633927861114 0 71.29282274080903 -en 592.1319535785387 0 91.58980409930733 -en 699.190001339254 0 117.46780571666169 -en 825.6042509899493 0 150.1042891583789 -en 974.8743229457496 0 190.7225217155683 -en 1151.1325728858374 0 240.479247750621 -en 1359.2584901053735 0 300.2977569564728 -en 1605.013780953549 0 370.64448651510696 -en 1895.2018727837517 0 451.25921707748773 -en 2237.856261592261 0 540.866179335767 -en 2642.4629066695265 0 636.9141207474848 -en 3120.2228358028515 0 735.4130877903922 -en 3684.3622360576646 0 830.9470871025904 -en 4350.498603166347 0 916.936026141531 -en 5137.073090297949 0 986.1897121260888 -en 6065.861027736246 0 1031.7388324716105 -en 7162.574752388678 0 1047.84990137343 |gzip>HN.hard_0.msOut.gz

How to speed up the simulation?

Hi，
I am running discoal to simulate hard, soft selection and neutral, but I found it is too slow for me, simulating one replicate need minutes, but I need to simulate 2000 replicates, so do you have any methods to speed it up? the command line for soft selection is :

discoal 12 2000 220000
-Pt 603.9255 5435.33
-Pr 1.732168 33764.92
-ws 0
-Pa 311.945 31194.5
-Pu 0 0.004007117
-Pf 0.01 0.2
-x 0.045454545454545456
-en 0.068638576 0 0.359088596
-en 0.108178701 0 0.288833244
-en 0.134816126 0 0.221769039
-en 0.156125998 0 0.22265817
-en 0.173016929 0 0.219402508
-en 0.191735252 0 0.137347905
-en 0.225324644 0 0.258311857 >> soft_0.msOut

Thanks!

Serial Sampling

I am very interested in using discoal to run simulations for time series data. I would be excited to see serial sampling incorporated so I could analyze samples collected before, during, and after a selective sweep.

Simulating purifying selection

Dear Prof. Kern,

   I'm wondering if there is a way to use discoal to simulate purifying selection on a genomic region where deleterious mutations are being removed with a user defined alpha=4Ns. 
   Does it equal to setting a hard sweep occurred many generations ago? Would selection continue to act on the position specified by -x, removing deleterious mutations after the beneficial allele got fixed?

Best regards,
Rongfeng Cui

Problematic newicks when both -c and -en in use

I'm working on simulating selection conditioned on present-day freq (-c mode) and changing demography (-en)

I get the following extremely odd errors in tree mode:

./discoal 2 100 1 -c 0.99 -wn 0 -i 1 -T | grep '\['
[1](1:1.821753,0:1.821753);
[1](1:0.110785,0:0.110785);
[1](1:0.177698,0:0.177698);
[1](0:0.335563,1:0.335563);
[1](0:0.148914,1:0.148914);
[1](0:0.632295,1:0.632295);

(i.e., these trees look fine)
However, the following ought to be equivalent, but I get completely different trees:

$ ./discoal 2 100 1 -c 0.99 -wn 0 -en 0.1 0 1 -i 1 -T | grep '\['
[1](0:0.100000,1:0.100000);
[1](0:0.100000,1:0.100000);
[1](0:0.076275,1:0.076275);
[1](1:0.100000,0:0.100000);
[1](0:0.100000,1:0.100000);

I find that making a call to -en at a particular time, it causes the vast majority of trees to coalescent at that exact time. In practice, this happens when i do e.g. "-en 0.1 0 0.55" but i'm just trying to make a poitn that "-en 0.1 0 1" ought to have the same behavior as no -en call whatsoever. Am I missing something?

maxmuts

Hi -
I'm interested in using the program and was testing it out using the code provided in the shic paper. I can get the equilibrium neutral models to produce output but I get an error when trying to run the Tennessen models. From your supplemental table:
discoal_multipop 170 1000 110000 -Pt 10560 31680 -r 17600
The error I get is
Assertion failed: (size < MAXMUTS), function makeGametesMS, file discoalFunctions.c, line 2048. Abort trap: 6
I tried recompiling discoal with a larger value of MAXMUTS but that didn't help. Do you have any suggestions?
Thanks!

ancient samples bug

seeing some strange output when multiple ancient samples are defined. there might be a bug but i'm not certain yet. USERS BEWARE.

Error: trajectory too bigly

I running simulations provided by the article 'soft sweeps are the dominant mode of adaptation in the human genomes'. I am using PEL population as an example. However when I run the command (provided in the supplementary material), the script runs for a while and then ends with the following error:

trajectory too bigly. step= 500000000 freq = 0.015251. killing myself gently

The command I ran is:

./discoal 170 50 200000 -Pt 40 400 -Pre 183.333 550 -en 0.0511027 0 0.901143 -en 0.083915 0 0.864485 -en 0.122773 0 1.06039 -en 0.168789 0 1.58688 -en 0.223285 0 2.81673 -en 0.28782 0 4.82159 -en 0.364248 0 7.19025 -en 0.454755 0 9.06247 -en 0.561862 0 9.83074 -en 0.688627 0 9.70829 -en 0.838705 0 8.64111 -en 1.01638 0 7.26809 -en 1.22674 0 6.05683 -en 1.47579 0 5.23362 -en 1.77063 0 4.74448 -en 2.11971 0 4.47973 -en 2.53297 0 4.39674 -en 3.02225 0 4.42625 -en 3.60152 0 4.6542 -en 4.2873 0 5.13193 -en 5.09922 0 6.01236 -en 6.06048 0 7.34732 -en 7.1985 0 8.79895 -en 8.5458 0 9.64914 -en 10.1409 0 9.63931 -en 12.0294 0 8.66812 -ws 0 -Pa 41.6667 833.333 -Pu 0 0.12 -Pf 0 0.2 -x 0.5

Could you tell me why am I getting this error? I am using the same command as mentioned in the article. The only difference is number of replicates. Also, the commands run fine for hard sweeps. It is for soft sweeps, I'm getting this error.

Can discoal simulate non-random mating such as inbreeding/selfing?

Hello,

I have a question: Can discoal simulate non-random mating such as inbreeding/selfing?

I could not find a coalescence simulator that has such functions. Not sure if this is limited by the theory or people just forgot about it...

Thanks!

Shujun

Trajectory failure

This command works with 0.1.2 and 0.1.1, but is failing on current master with a trajectory failure:

discoal 100 500 1000 -ws 0 -t 100 -r 100 -a 2000 -x 0.5