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Individual-based forward-time genetics simulation software
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From: Fred G. <gui...@gm...> - 2020-12-10 09:49:47
|
N E M O v2.3.53 [04 DEC 2020] This is a bug fix release. A bug affected the speed of the simulations when free recombination was chosen for the quanti and ntrl traits, slowing down the simulations substantially. FG |
From: Frederic G. <gui...@gm...> - 2020-09-09 18:56:24
|
Dear nemo users, I'm happy to announce the release of version 2.3.52. The changelog is copied below. I take this opportunity to also announce that starting now, the mailing lists are moved to google groups. This mailing list will be discontinued in the near future. So, register to : - nemo-simul to post questions, requests, comments etc https://groups.google.com/g/nemo-simul - nemo-announce to receive notices about new versions and new products https://groups.google.com/g/nemo-announce === CHANGELOG === N E M O v2.3.52 [26 Aug 2020] This release improves parameter consistency checks at startup for enhanced user's experience and parameter debugging. It also introduces new functionalities, updates error and warning messages and addresses a few performance issues under the hood. New features: At startup, Nemo warns about orphan parameters (parameters that don't belong to any component), missing mandatory parameters (once at least one parameter of a component is set), and prompts for an abort when mandatory parameters area missing. Wright-Fisher populations : It is now easier to model Wright-Fisher populations (i.e., populations with constant patch sizes and random mating) without migration in the breed LCE (previously handled by breed_disperse). new parameter in the "breed" LCE: *mating_isWrightFisher* Population sub-sampling for file output: You can now save the genotypes of a sample of the individuals within each patch instead of the whole population. new parameters in the "save_files" LCE: *files_sample_size* *files_sample_age* The trait genetic maps can have variable numbers of loci per chromosome: The parameter (trait)_genetic_map accepts variable matrices, i.e, matrices with rows of different lengths. Yet, all traits must have the same number of chromosomes (no empty chromosome allowed for a given trait). CHANGELOG v2.3.52 ADD: population sub-sampling of individuals for genotype file output ADD: faster Wright-Fisher mating model (i.e., populations with constant patch sizes and random mating) in LCE breed (no dispersal). ADD: shortcut to pass the identity matrix as dispersal matrix (manual p43) MOD: *_genetic_map accept variable matrix in imput (diff num loci/chroms) MOD: better param consistency check at start up: now issues warnings when mandatory params are missing, or for unset/unfound parameters FIX: better memory management, addressing rare cases of double de-alloc or memory leaks |
From: Fred G. <gui...@gm...> - 2020-08-24 14:00:16
|
Dear Nathan, Thanks! To solve your problem, you could add one (or two) "neutral" QTL on the last chromosome. To do so, you'd have to have di-allelic loci and set the allelic effects to 0 for the QTL on chromosome 6, with something like: quanti_loci 11 quanti_allele_model diallelic_HC quanti_allele_value {{a, a, a, a, a, a, a, a, a, a, 0}} # alleles have value +/- a (loc 1 - 10) or 0 (loc 11) quanti_chromosome_num_locus {{2, 2, 2, 2, 2, 1}} ... that should work! tell us if not (I haven't tested it) On the other hand, there is no way around this limitation if you can't simulate di-allelic loci, because there is no locus-specific mutation model for the continuous allele model (yet). I hope this helps. Best, Fred On 8/24/20 3:10 PM, Nathan White wrote: > Dear Fred (et al) > > I'm a PhD student at the University of Sheffield and have been using > Nemo for a few months now- it's very useful, thank you very much for > developing it! > > I've encountered a problem with the genetic map- I'm trying to simulate > 6 chromosomes with 100 neutral sites each, then place 2 quant loci on > each chromosome except for one (so it has only neutral sites). > > My code has the relevant lines, e.g. > ntrl_loci 600 > ntrl_random_genetic_map {{100, 100, 100, 100, 100, 100}} > > quanti_random_genetic_map {{100, 100, 100, 100, 100, 100}} > quanti_chromosome_num_locus {{2, 2, 2, 2, 2, 0}} > quanti_loci 10 > > But when I run it, I get the error > ***ERROR*** the genetic map doesn't accept empty chromosomes with 0 loci > ***ERROR*** initialization of prototype for trait "quant" failed > > Is there a way around this? To have a chromosome with neutral loci but > no quanti loci? > > Thanks very much > Nathan > -- > Nathan White > PhD Student > Dept. Animal & Plant Sciences > University of Sheffield > @NJWhite_Evo > > > > _______________________________________________ > Nemo2-user mailing list > Nem...@li... > https://lists.sourceforge.net/lists/listinfo/nemo2-user > |
From: Nathan W. <nw...@sh...> - 2020-08-24 13:32:45
|
Dear Fred (et al) I'm a PhD student at the University of Sheffield and have been using Nemo for a few months now- it's very useful, thank you very much for developing it! I've encountered a problem with the genetic map- I'm trying to simulate 6 chromosomes with 100 neutral sites each, then place 2 quant loci on each chromosome except for one (so it has only neutral sites). My code has the relevant lines, e.g. ntrl_loci 600 ntrl_random_genetic_map {{100, 100, 100, 100, 100, 100}} quanti_random_genetic_map {{100, 100, 100, 100, 100, 100}} quanti_chromosome_num_locus {{2, 2, 2, 2, 2, 0}} quanti_loci 10 But when I run it, I get the error ***ERROR*** the genetic map doesn't accept empty chromosomes with 0 loci ***ERROR*** initialization of prototype for trait "quant" failed Is there a way around this? To have a chromosome with neutral loci but no quanti loci? Thanks very much Nathan -- Nathan White PhD Student Dept. Animal & Plant Sciences University of Sheffield @NJWhite_Evo |
From: Francois L. (PACA) <fra...@in...> - 2020-07-08 17:56:06
|
OK nice ! This is clear Cheers, FL Le 08/07/2020 à 18:15, Fred Guillaume a écrit : >> For 1/ this is what I understood >> For 2/ OK I will disregard those migration stats. >> For final clarification on this 2nd point: as you correctly understood >> there is both pollen and seed dispersal (different migration rates), do >> you mean that in such case the migration stats cumulate pollen grains >> and zygotes (seeds) together? > actually no! I had to check the code: each dispersal LCE resets the > counters before execution > so, moving save_stats up and down your life cycle will let you isolate > the effect of each LCE > cheers > F -- François Lefèvre INRAE, Ecologie des Forêts Méditerranéennes, URFM, 84914 Avignon, France Domaine Saint Paul, 228 route de l'Aérodrome Agroparc +33 (0)4 32 72 29 01 |
From: Fred G. <gui...@gm...> - 2020-07-08 16:15:51
|
> For 1/ this is what I understood > For 2/ OK I will disregard those migration stats. > For final clarification on this 2nd point: as you correctly understood > there is both pollen and seed dispersal (different migration rates), do > you mean that in such case the migration stats cumulate pollen grains > and zygotes (seeds) together? actually no! I had to check the code: each dispersal LCE resets the counters before execution so, moving save_stats up and down your life cycle will let you isolate the effect of each LCE cheers F |
From: Francois L. (PACA) <fra...@in...> - 2020-07-08 15:45:35
|
Dear Fred, many thanks for your quick answer, much appreciated too! Yes it helps! For 1/ this is what I understood For 2/ OK I will disregard those migration stats. For final clarification on this 2nd point: as you correctly understood there is both pollen and seed dispersal (different migration rates), do you mean that in such case the migration stats cumulate pollen grains and zygotes (seeds) together? Best, François Le 08/07/2020 à 16:06, Fred Guillaume a écrit : > Dear François, > > thanks for posting to the list, this is very much appreciated! > > the answers to your questions are: > > 1/ the *regulation* LCE independently regulates the offspring and adults > to the patch capacities - this is indeed why you have K offspring AND K > adults after regulation. > Note that regulation is also performed in the *aging* LCE where max K > offspring are chosen to become the new adult generation in each patch. > You may thus not need to add *regulation* in your life cycle. > > 2/ the number of residents (and other migration stats) is calculated > during migration, i.e., when the *disperse* LCE (or *breed_disperse* as > in your case) is executed in the life cycle. Therefore, the number of > residents depends on the number of offspring when dispersal is processed > and not when you record the stats (with *save_stats*). resid.pi will > exceed the number of adults when fecundity is high and migration rates > are low. > > Now, your case is special because you mix forward (seed) and backward > (pollen) migration. Thus, residents are counted during each event and > will largely exceed the carrying capacities. In your case I would > disregard those stats, or you can place *save_stats* inbetween the two > dispersal LCEs to isolate their effect on the migration counters. Note > that for backward migration, a resident is a pollen grain that > originated from a local parent. In that case, each parent (adult) can be > both a resident or a migrant depending on where it sends its pollen grains. > > I hope this helps! > > Best, > Fred > > > On 7/8/20 2:56 PM, Francois Lefevre (PACA) wrote: >> Hello, >> (sorry if this mailing list is not the appropriate way to post these >> questions, if it is not just tell me) >> >> two questions about the population stat outputs: >> >> 1) for each patch /i/, both statistics of the nb of offspring >> (/off.fem.pi)/ and nb of adults (/adlt.fem.pi)/ can reach the patch >> capacity eventhough they are computed after the regulation step (see >> Life cycle below): do I correctly understand that population regulation >> is made independently for offspring and adults? >> (after aging and mortality of the adults, only the younger cohort is >> kept and becomes adult, ending to the appropriate capacity) >> >> 2) how is computed the number of residents per patch (/resid.pi)/ ? This >> number largely exceeds the carrying capacity and also exceeds the number >> of adults of the patch: does it represent the "memory" of the total >> number of local individuals before regulation, i.e. nb of adults and >> locally produced offspring? >> >> The Life cycle is the following: >> breed_disperse 1 >> seed_disp 2 >> viability_selection 3 >> regulation 4 >> save_stats 5 >> store 6 >> aging 7 >> save_files 8 >> >> Thank you! >> François >> >> -- >> François Lefèvre >> INRAE, Ecologie des Forêts Méditerranéennes, URFM, 84914 Avignon, France >> Domaine Saint Paul, 228 route de l'Aérodrome Agroparc >> +33 (0)4 32 72 29 01 >> >> >> >> _______________________________________________ >> Nemo2-user mailing list >> Nem...@li... >> https://lists.sourceforge.net/lists/listinfo/nemo2-user >> -- François Lefèvre INRAE, Ecologie des Forêts Méditerranéennes, URFM, 84914 Avignon, France Domaine Saint Paul, 228 route de l'Aérodrome Agroparc +33 (0)4 32 72 29 01 |
From: Fred G. <gui...@gm...> - 2020-07-08 14:07:05
|
Dear François, thanks for posting to the list, this is very much appreciated! the answers to your questions are: 1/ the *regulation* LCE independently regulates the offspring and adults to the patch capacities - this is indeed why you have K offspring AND K adults after regulation. Note that regulation is also performed in the *aging* LCE where max K offspring are chosen to become the new adult generation in each patch. You may thus not need to add *regulation* in your life cycle. 2/ the number of residents (and other migration stats) is calculated during migration, i.e., when the *disperse* LCE (or *breed_disperse* as in your case) is executed in the life cycle. Therefore, the number of residents depends on the number of offspring when dispersal is processed and not when you record the stats (with *save_stats*). resid.pi will exceed the number of adults when fecundity is high and migration rates are low. Now, your case is special because you mix forward (seed) and backward (pollen) migration. Thus, residents are counted during each event and will largely exceed the carrying capacities. In your case I would disregard those stats, or you can place *save_stats* inbetween the two dispersal LCEs to isolate their effect on the migration counters. Note that for backward migration, a resident is a pollen grain that originated from a local parent. In that case, each parent (adult) can be both a resident or a migrant depending on where it sends its pollen grains. I hope this helps! Best, Fred On 7/8/20 2:56 PM, Francois Lefevre (PACA) wrote: > Hello, > (sorry if this mailing list is not the appropriate way to post these > questions, if it is not just tell me) > > two questions about the population stat outputs: > > 1) for each patch /i/, both statistics of the nb of offspring > (/off.fem.pi)/ and nb of adults (/adlt.fem.pi)/ can reach the patch > capacity eventhough they are computed after the regulation step (see > Life cycle below): do I correctly understand that population regulation > is made independently for offspring and adults? > (after aging and mortality of the adults, only the younger cohort is > kept and becomes adult, ending to the appropriate capacity) > > 2) how is computed the number of residents per patch (/resid.pi)/ ? This > number largely exceeds the carrying capacity and also exceeds the number > of adults of the patch: does it represent the "memory" of the total > number of local individuals before regulation, i.e. nb of adults and > locally produced offspring? > > The Life cycle is the following: > breed_disperse 1 > seed_disp 2 > viability_selection 3 > regulation 4 > save_stats 5 > store 6 > aging 7 > save_files 8 > > Thank you! > François > > -- > François Lefèvre > INRAE, Ecologie des Forêts Méditerranéennes, URFM, 84914 Avignon, France > Domaine Saint Paul, 228 route de l'Aérodrome Agroparc > +33 (0)4 32 72 29 01 > > > > _______________________________________________ > Nemo2-user mailing list > Nem...@li... > https://lists.sourceforge.net/lists/listinfo/nemo2-user > |
From: Francois L. (PACA) <fra...@in...> - 2020-07-08 13:12:31
|
Hello, (sorry if this mailing list is not the appropriate way to post these questions, if it is not just tell me) two questions about the population stat outputs: 1) for each patch /i/, both statistics of the nb of offspring (/off.fem.pi)/ and nb of adults (/adlt.fem.pi)/ can reach the patch capacity eventhough they are computed after the regulation step (see Life cycle below): do I correctly understand that population regulation is made independently for offspring and adults? (after aging and mortality of the adults, only the younger cohort is kept and becomes adult, ending to the appropriate capacity) 2) how is computed the number of residents per patch (/resid.pi)/ ? This number largely exceeds the carrying capacity and also exceeds the number of adults of the patch: does it represent the "memory" of the total number of local individuals before regulation, i.e. nb of adults and locally produced offspring? The Life cycle is the following: breed_disperse 1 seed_disp 2 viability_selection 3 regulation 4 save_stats 5 store 6 aging 7 save_files 8 Thank you! François -- François Lefèvre INRAE, Ecologie des Forêts Méditerranéennes, URFM, 84914 Avignon, France Domaine Saint Paul, 228 route de l'Aérodrome Agroparc +33 (0)4 32 72 29 01 |
From: fred <gui...@gm...> - 2019-02-14 11:15:58
|
Dear Natasha most likely reason is that you have a syntax error in your .ini file if you look closely at the messages, nemo didn't include any trait in the simulation and the only life cycle event is 'save_files' also, the file that nemo tries to load the population from is called "C:source_file_type", which is a bit weird because 'source_file_type' is a parameter name so, make sure you didn't make any syntax error in the parameter file! it is difficult to help without having a look at the ini file best Fred On 12/02/2019 23:54, Natasha Serrao wrote: > Hello All: > I am trying to load my source population into Nemo2 and keep getting the > following error (see attached). I have changed the source_pop extension > to .txt and changed the source_file_type to .txt. > > Any thoughts on what the problem might be? > > Thank you, > Natasha > > > > _______________________________________________ > Nemo2-user mailing list > Nem...@li... > https://lists.sourceforge.net/lists/listinfo/nemo2-user > |
From: Natasha S. <nat...@gm...> - 2019-02-12 22:55:21
|
Hello All: I am trying to load my source population into Nemo2 and keep getting the following error (see attached). I have changed the source_pop extension to .txt and changed the source_file_type to .txt. Any thoughts on what the problem might be? Thank you, Natasha |
From: Frederic G. <gui...@gm...> - 2019-01-27 15:35:16
|
Dear users I have uploaded a new package "Nemo-2.3.51-Win64.tgz" with the Windows version of nemo2.3.51. Nemo has been compiled on Windows 10 using Cygwin 2.11.2. You will find the executabe in the folder 'Nemo-2-3-51/bin'. To run Nemo on a Windows machine, use Cygwin (www.cygwin.com). When installing Cygwin, make sure you choose the 'libgsl19' package (use the search menu within the Cygwin installer to find it). Nemo needs that library to work. *** To compile Nemo with Cygwin, the following Cygwin packages are necessary: - gcc-core - gcc-g++ - make - libgsl-devel - libgsl19 - makedepend (optional) (see attached picture) Compiling Nemo from the Cygwin terminal is rather straightforward (see attached pics): 1. launch the Cygwin terminal. Your working directory will then be your home directory in C:/cygwin64/home/USER (replace USER with your Windows user name) 2. download the nemo source package from sourceforge.net into your cygwin home directory 3. un-tar the package with the following command (don't type the leading $): $ tar xzf Nemo-2.3.51-src.tgz 4. move to the Nemo-2.3.51 folder: $ cd Nemo-2.3-51 5. add execution permission to the script 'getVersion.sh' $ chmod +x getVersion.sh 6. compile Nemo: $ make WIN=1 the executable will be placed in the 'bin' folder in Nemo-2.3.51 (your current working directory) 7. run Nemo with an example file: $ bin/nemo2.3.51 example/Nemo2.ini 8. that's it! you can then copy the program file 'nemo2.3.51' where you want it to be to run your simulations. Enjoy, and post questions on le mailing list. Thanks for using Nemo! \fg |
From: fred <gui...@gm...> - 2019-01-27 10:11:26
|
Dear Natasha You get this message because you don't have execution right for the file 'nemo2.3.51'. Your system thus considers this file as a regular file and not an executable. To change this, on linux, use the following command: $ chmod +x nemo2.3.51 you can then start nemo with $ ./nemo2.3.51 I hope this helps cheers Fred On 27/01/2019 00:25, Natasha Serrao wrote: > HI Everyone: > > I came across this message and was wondering if anyone had seen this before? > > I keep getting "permission denied"? > > Thank you, > Natasha Serrao > > image.png > **//___^ > > > _______________________________________________ > Nemo2-user mailing list > Nem...@li... > https://lists.sourceforge.net/lists/listinfo/nemo2-user > |
From: Natasha S. <nat...@gm...> - 2019-01-26 23:25:59
|
HI Everyone: I came across this message and was wondering if anyone had seen this before? I keep getting "permission denied"? Thank you, Natasha Serrao [image: image.png] |
From: Natasha S. <nat...@gm...> - 2019-01-25 19:11:34
|
Hi Everyone: I am trying to use Nemo-2 on Windows using Cygwin and am having a hard time getting it to work. I have typed in the following command on windows 10 and couldn't get it to work. Any suggestions? Thanks so much, Natasha Serrao |
From: Frederic G. <gui...@gm...> - 2018-10-03 17:06:12
|
Dear all, Nemo v2.3.51 has just been released! See the changelog below I recommend updating to the new version. Have fun with it! Post comments/questions on the mailing list. Best Fred Guillaume N E M O v2.3.51 [27 Sept 2017] This new release fixes a few bugs and add new functionalities to Nemo. It also introduces new parameters and updates error and warning messages. The MPI layer has also been updated and is now fully funcitonal. New parameters: - "disperse" LCE: "dispersal_lattice_rows": sets the number of rows of the 2D lattice "dispersal_lattive_columns": sets the number of columns of the 2D lattice - "delet" trait: "delet_effects": a matrix holding the fitness effects of the mutations "delet_backmutation_rate": rate of backward mutations, reversing the locus state to the wild type (with fitness = 1); is 0 by default - "population" component: "source_parameter_override": sets parameter value from value stored in a binary source files, overriding the current simulation parameter values CHANGELOG v2.3.51 FIX: segfault when input FSTAT file contained allele '0'; allele '0' not accepted anymore in input genotype files FIX: names of trait genetic covariance stats for trait 'quanti' corrected in stat output files FIX: parameter with multiple external parameter files specified in the input file now correctly treated as a sequential parameter FIX: output binary files can now be > 2.1GB; however, file format is NOT COMPATIBLE with older versions of Nemo. FIX: parameter temporal values correctly reset between different simulations ADD: dispersal lattice model (dispersal_model 4) now accepts arbitrary number of rows and columns (previously limited to square grids) ADD: backward mutation rate in deleterious-mutation trait (delet) ADD: direct setting of mutation fitness effect in deleterious-mutation trait with new parameter "delet_effects"; could only be set randomly from a specified distribution so far ADD: possibility to load random deleterious mutation effects from binary source files via parameter "source_parameter_override" ADD: "source_parameter_override" to set parameter value from binary source files, overriding the loading simulation parameter values ADD: PLINK output file format for neutral markers (.ped, .fam, .map, .bin) ADD: new warnings at start when nemo finds orphan parameters in the input parameter file (i.e., parameters that don't belong to any component) ADD: possibility to execute an external shell script after each replicates instead of after all simulations in a run. ADD: locus-specific alleles values of quantitative trait now recycled across loci if less values than number of loci provided in input MOD: the fitness effects of the deleterious mutations are now saved in the `.log' file of the simulation after being randomly set during setup MOD: runtime messaging about existing simulation files, and other messages have been refreshed and updated MOD: MPI version and random number generator adjusted for SPRNG v5.0; MPI version fully functional! /fg |
From: Frederic G. <gui...@gm...> - 2018-10-03 17:01:19
|
Hi Carolina, Welcome to Nemo! You are using a very old version of Nemo that I would not advise to use anymore. I don't understand why you can't get the latest version from sourceforge... I have just released a new version of Nemo (v2.3.51), may it will work with that new version? Ask me directly if you still have problems I hope it works all the best, Fred Guillaume ----- Hi folks I am new in Nemo and I try to simulate my phd data but unfortunally I got several errors. The program Nemo 2.2.0.exe runs correctly for some short computations. But when it attempts a longer computation, it crashes after a few minutes with the error: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc 2 [sig] nemo2.2.0 17160 open_stackdumpfile: Dumping stack trace to nemo2.2.0.exe.stackdump Any idea what could cause this error? I am using a old versio becauseI did not get the latest version - Nemo 2.3.46. Thanks! -- Dr. Carolina Machado Posdoctoral researcher Federal University of São Carlos Department of Genetic and Evolution Molecular Biodiverstity and Conservation Laboratory Address: Rodovia Washington Luís, Km235 - SP-310 CEP: 13565-905 Phone: (16) 3351-8309 (Lab) |
From: Carolina M. <car...@gm...> - 2018-09-14 18:15:17
|
Hi folks I am new in Nemo and I try to simulate my phd data but unfortunally I got several errors. The program Nemo 2.2.0.exe runs correctly for some short computations. But when it attempts a longer computation, it crashes after a few minutes with the error: terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc 2 [sig] nemo2.2.0 17160 open_stackdumpfile: Dumping stack trace to nemo2.2.0.exe.stackdump Any idea what could cause this error? I am using a old versio becauseI did not get the latest version - Nemo 2.3.46. Thanks! -- Dr. Carolina Machado Posdoctoral researcher Federal University of São Carlos Department of Genetic and Evolution Molecular Biodiverstity and Conservation Laboratory Address: Rodovia Washington Luís, Km235 - SP-310 CEP: 13565-905 Phone: (16) 3351-8309 (Lab) |
From: frederic g. <gui...@gm...> - 2017-04-27 07:59:42
|
Dear Ivan, (I redirect this to the mailing list) thanks for reporting this bug the default file extension of the neutral trait has recently switched from '.dat' to '.txt' to call the reader for neutral trait input files use: source_file_type .txt and rename your .dat file as a .txt file BUT keep the file as a regular FSTAT file, as this is the only input format recognized at the moment I hope this helps Best Fred -------- Forwarded Message -------- > Subject: Re: Nemo > Date: Thu, 27 Apr 2017 01:38:41 -0300 > > Dear Fred, > > I am running Nemo in Windows and so far I have been able to evalute > different scenarios with random allelic values, but every time I try to > run Nemo with my own data (fstat file) I receive an error like this one: > > " replicate 1/20 [01:28:44] 1/100 ***ERROR*** no file reader exists > with source file extension ".dat"." > > Can you please help me to find out what is wrong with my .ini file > and/or my fstat file (attached in this email)? > > > Regards, > > > Iván |
From: frederic g. <gui...@gm...> - 2017-02-20 10:07:00
|
Dear Luke, I'm now forwarding this thread to the mailing list as other users may be interested as well So, there seems to be a problem on Mac OSX 10.12.3 (with llvm-gcc 4.2.1), which causes a) an error when compiling (scroll to bottom) and b) crashes on certain occasions (hard to determine when exactly) I could not reproduce any of those problems on previous OSX version (10.7.5 with llvm-gcc 4.2.1) or other systems (Linux Debian 8 jessie with gcc 4.9.2) The ini files attached all ran fine when I used nemo2.3.46r7 on them. Could you please send me the crash reports of your failed runs? You should find them in the 'Console' application in /Applications/Utilities/ under the "User Diagnostic Reports" category in Console (if still the same under OS X 10.12...) I am sorry I cannot do more for now, I don't currently have access to a more recent Mac The only solution I can think of now is that you should select a different (earlier) SDK than the 10.12 version in XCode. For this you need to create an XCode project for nemo and compile it wihtin XCode directly (or you find the gcc op. It may be a bit tricky to navigate all compiling options at first, but there is a section where you set the version of the C/C++ libraries to use (the SDK). This is found under the "Architectures" section. There, select an earlier version for the "Base SDK" (mine is Mac OS X 10.7). You can also set the target OS X version for which you compile your program under the "Deployment" section -> "Mac OS X Deployment Target" set it to something basic (if you have installed the necessary libraries), which should run on most OS X versions (hopefully...) I hope this works, let me know if not! Best, Fred -------- Forwarded Message -------- > From: Luke Holman <L.E...@so...> > To: Frederic Guillaume <fre...@ie...> > Subject: Re: nemo Installation (more) Woes > Date: Wed, 15 Feb 2017 10:46:31 +0000 > > Hi Fred, > > > I’m hoping you can once again provide some assistance on Nemo. > > > After following your advice nemo compiled. However I’m having some > problems running simulations. > > > I can get the ‘multiselection.ini’ example to work, but not the > ‘matrix-example.ini’ or my own simulation ‘test_1.ini’. All are > attached. > > > Those that do not work produce the following error. The main > difference I can see between the runs is those that do not work have > dispersal LCE included in the cycle. > > > I appreciate this may be quite hard to debug, maybe I should shift to > the linux version if there are too many problems on mac os x? > > > > > Lukes-MacBook-Pro-2:bin Luke$ ./nemo2.3.46 matrix-example.ini > > > N E M O 2.3.46r7 [09 Feb 2017] > > > Copyright (C) 2006-2017 Frederic Guillaume > This is free software; see the source for copying > conditions. There is NO warranty; not even for > MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. > http://nemo2.sourceforge.net > ------------------------------------------------ > reading parameters from "matrix-example.ini" > setting random seed from input value: 65466 > Segmentation fault: 11 > > > Thanks, > > > Luke > > > > > > > > ************************************* > Luke Holman > PhD Candidate > > > National Oceanography Centre > University of Southampton > > > > > > > > > > > > On 12 Feb 2017, at 22:03, Luke Holman <L.E...@so...> > > wrote: > > > > Hi Fred, > > > > > > I’m using the latest (10.12.3) version of OSX, 'gcc —version' > > returns the below. I have a the apple Xcode libraries installed so I > > think the default gcc is some kind of apple version. *sigh* > > > > > > Configured with: > > --prefix=/Applications/Xcode.app/Contents/Developer/usr > > --with-gxx-include-dir=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/c++/4.2.1 > > Apple LLVM version 8.0.0 (clang-800.0.42.1) > > Target: x86_64-apple-darwin16.4.0 > > Thread model: posix > > InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin > > > > > > I removed the parameter on the line you suggested and everything > > seemed to compile fine! Hopefully there are no strange side effects > > of leaving the parameter out. > > > > > > Thank you for your help, much appreciated. Looking forward to > > getting my head round the software , it seems like exactly the tool > > I’m after. > > > > > > Kind Regards, > > > > > > Luke > > > > > > > > ************************************* > > Luke Holman > > PhD Candidate > > > > > > National Oceanography Centre > > University of Southampton > > > > > > > > > > > > > > > > > > > > > > > On 11 Feb 2017, at 17:22, Frederic Guillaume > > > <fre...@ie...> wrote: > > > > > > Dear Luke > > > > > > interesting... I never had this error before, and this is an old > > > piece of code! > > > > > > what version of OSX and gcc do you use? (use command: gcc > > > --version) > > > > > > otherwise, removing "_genITER(0), " on that line in LCEmisc.cc > > > should solve the problem > > > > > > it seems it is a problem of the c++ libraries you are using > > > > > > I hope this works! > > > let me know > > > > > > best regards > > > Fred > > > > > > > > > -- > > > Frédéric Guillaume > > > SNSF Assistant Professor > > > Dept of Evolutionary Biology and Environmental Studies > > > University of Zurich > > > Winterthurerstrasse 190 > > > CH-8057 Zurich > > > tel: +41 (0)44 635 66 23 > > > office: Y25-G-78 > > > > > > http://www.ieu.uzh.ch/research/evolbiol/ecoevo.html > > > > > > > > > On 10 févr. 2017, at 17:45, Luke Holman wrote: > > > > > > > Dear Frédéric, > > > > > > > > I’m a PhD student at the University of Southampton working on > > > > invasion genomics. I want to use NEMO to simulate multi locus > > > > genotypes for some simple populations to test a hypothesis but > > > > I’m struggling to get the installation to work. Following the > > > > installation of gsl on my mac I get the below error when running > > > > the makefile. Do you have any suggestions? > > > > > > > > 246-82:Nemo-2.3.46 leh1n15$ make MAC=1 > > > > g++ -DHAS_GSL -w -O3 -funroll-loops -c src/LCEbreed.cc -o > > > > src/LCEbreed.o -I/usr/local/include > > > > g++ -DHAS_GSL -w -O3 -funroll-loops -c src/LCEcomposite.cc -o > > > > src/LCEcomposite.o -I/usr/local/include > > > > g++ -DHAS_GSL -w -O3 -funroll-loops -c src/LCEdisperse.cc -o > > > > src/LCEdisperse.o -I/usr/local/include > > > > g++ -DHAS_GSL -w -O3 -funroll-loops -c src/LCEmisc.cc -o > > > > src/LCEmisc.o -I/usr/local/include > > > > src/LCEmisc.cc:801:57: error: field of type > > > > 'list<int>::const_iterator' (aka '__list_const_iterator<int, > > > > void *>') has private constructor > > > > LCE_Resize::LCE_Resize() : LifeCycleEvent("resize",""), > > > > _genITER(0), _atGeneration(0), > > > > ^ > > > > /Library/Developer/CommandLineTools/usr/bin/../include/c > > > > ++/v1/list:394:14: note: implicitly declared private > > > > here > > > > explicit __list_const_iterator(__link_pointer __p) > > > > _NOEXCEPT : __ptr_(__p) {} > > > > ^ > > > > 1 error generated. > > > > make: *** [src/LCEmisc.o] Error 1 > > > > > > > > > > > > > > > > Thanks, > > > > > > > > Luke > > > > > > > > > > > > > > > > > > > > ************************************* > > > > Luke Holman > > > > PhD Candidate > > > > > > > > National Oceanography Centre > > > > University of Southampton > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > |
From: frederic g. <gui...@gm...> - 2017-02-10 09:02:53
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Hi all, I'm happy to announce the release of Nemo v2.3.46! download it here: https://sourceforge.net/projects/nemo2/files/Nemo/2.3.46/ CHANGELOG v2.3.46 FIX: recombination between 2 first loci on the genetic map was suppressed if chromosome-wide recombination rates were specified as a round log 10 number in the input file (e.g. ..._recombination_rate 0.001) FIX: corrected handling of the quadratic fitness option for quantitative trait, a bug existed when several traits were specified FIX: composite life cycle breed_selection_disperse was ignoring traits not under selection -> no inheritance done! ADD: now possible to save the pedigree information for the whole population or for a sample of each patch to a text file ('pop_output...' params) ADD: now possible to load a population from a pedigree file (from real or simulated pedigrees) and perform genetic simulations (mutation and recombination) with the individuals contained in the pedigree file (using the 'cross' life cycle event operator) ADD: new file output to save the whole population distribution of individual fitness values when selection is used in the life cycle ADD: new file output to save allele frequency changes at diallelic quantitative loci in each patch across generations with quanti_freq_output options ADD: local relative fitness scaling can now be done relative to the maximum fitness value in a patch instead of relative to its mean fitness value MOD: chromosomes may have a variable number of loci on all genetic maps MOD: configuration file: change of '@' -> '&' to pre-pend the name of external files (files containing large parameter values like matrices) to avoid confusion with temporally varying parameters arguments and potential runtime errors MOD: the content of the external parameter files is not written to the '.log' and '.bin' files anymore |
From: frederic g. <gui...@gm...> - 2016-07-15 16:00:00
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Dear Tom, I'm glad you managed to load the info into Nemo. The default file type for the ntrl trait has indeed changed to ".txt" to match the default output format, which is the tabular format. Somehow, the default input format is still the FSTAT format, which is why it worked in your case. I will change that in the next release to allow for more control on input/output formats. But, this said, you cannot use the ".dat" file to set the wolbachia trait, it is only for the neutral markers. I am surprised that it worked in your case... Concerning Wolbachia, there is currently no other way to set initial infection frequencies than to use the 'wolbachia_inoculum_size' and 'wolbachia_inoculum_time' parameters. I see that some code change hasn't been properly documented. The infection "inoculum" is the same in each patch but in females only. I attach a modified version of the code that allows for patch-specific inoculum. Move these files to the source directory of Nemo2.3.45 and recompile. It should work. i also attach a corrected version of your Nemo2.ini file. Several mistakes prevent the simulation to run properly. You will now also see how to specify initial frequencies of wolbachia differently in each patch and for males and females by providing a matrix as argument to wolbachia_inoculum_size (each row for a patch, {female, male} size of inoculum) I hope this helps. Unfortunately, I will be on holiday for the next 2.5 weeks and will not be able to answer questions or correct bugs. Best, FG On Fri, 2016-07-15 at 17:09 +0200, frederic guillaume wrote: > > > > Dear Dr. Guillaume, > > As a follow-up to this, I have now managed to get Nemo to recognise the > population file by registering it as .txt, and to get breed_wolbachia to > work by setting all the breeding and Wolbachia parameters. > > However, what I really want to do is to assign Wolbachia frequencies on > a patch-by-patch basis, so that some patches start with the infection > and others do not. It seems like this option should be accommodated by > Nemo2.3.45, but it doesn't seem like I can load Wolbachia infection data > from a population file, like I could for age/sex/etc. Is a > patch-by-patch infection rate able to handled by Nemo? > > This would be a great feature as it would mean one could model the sweep > of Wolbachia through a population. > > Regards > Tom Schmidt > > > > ---------- Forwarded message ---------- > From: Tom Schmidt <t.l...@gm...> > Date: Thu, Jul 14, 2016 at 11:16 AM > Subject: Problem with .dat file > To: nem...@li... > > > Dear Dr Guillaume, > > I am looking forward to using Nemo2.3.45 for the first time to analyse a > spread of disease-blocking Wolbachia, which would be part of a > substantial part of my research. > > I've put together all my files to run in lubuntu, but I consistently get > the error message: "no file reader exists with source file > extension .dat" > > I realise someone also asked this question before, but I've found no > solution to my problem. As it is my .init file and its contents seem to > be recognised but the program won't locate/read/accept the .dat file I > have in the same location. > > All that I need the .dat file for is to specify initial Wolbachia > infection rates on a patch-by-patch basis. Is there a way to do this in > the .init file itself, as if there is I can dispense with the .dat file? > > Additionally, I am using breed_wolbachia as a LCE, but it doesn't seem > to be recognised by the program. When I just input "breed", it is > recognised (but the program still stops when it can't find the .dat > file). > > I look forward to hearing from you. I ahve attached my input files, and > a copy of the output reading, if it may help in your answering my query. > I thank you in advance for any help you're able to give me. > > Regards > Tom Schmidt > University of Melbourne > > |
From: Tom S. <t.l...@gm...> - 2016-07-14 02:33:40
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Dear Dr. Guillaume, As a follow-up to this, I have now managed to get Nemo to recognise the population file by registering it as .txt, and to get breed_wolbachia to work by setting all the breeding and Wolbachia parameters. However, what I really want to do is to assign Wolbachia frequencies on a patch-by-patch basis, so that some patches start with the infection and others do not. It seems like this option should be accommodated by Nemo2.3.45, but it doesn't seem like I can load Wolbachia infection data from a population file, like I could for age/sex/etc. Is a patch-by-patch infection rate able to handled by Nemo? This would be a great feature as it would mean one could model the sweep of Wolbachia through a population. Regards Tom Schmidt ---------- Forwarded message ---------- From: Tom Schmidt <t.l...@gm...> Date: Thu, Jul 14, 2016 at 11:16 AM Subject: Problem with .dat file To: nem...@li... Dear Dr Guillaume, I am looking forward to using Nemo2.3.45 for the first time to analyse a spread of disease-blocking Wolbachia, which would be part of a substantial part of my research. I've put together all my files to run in lubuntu, but I consistently get the error message: "no file reader exists with source file extension .dat" I realise someone also asked this question before, but I've found no solution to my problem. As it is my .init file and its contents seem to be recognised but the program won't locate/read/accept the .dat file I have in the same location. All that I need the .dat file for is to specify initial Wolbachia infection rates on a patch-by-patch basis. Is there a way to do this in the .init file itself, as if there is I can dispense with the .dat file? Additionally, I am using breed_wolbachia as a LCE, but it doesn't seem to be recognised by the program. When I just input "breed", it is recognised (but the program still stops when it can't find the .dat file). I look forward to hearing from you. I ahve attached my input files, and a copy of the output reading, if it may help in your answering my query. I thank you in advance for any help you're able to give me. Regards Tom Schmidt University of Melbourne |
From: Tom S. <t.l...@gm...> - 2016-07-14 01:16:43
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Dear Dr Guillaume, I am looking forward to using Nemo2.3.45 for the first time to analyse a spread of disease-blocking Wolbachia, which would be part of a substantial part of my research. I've put together all my files to run in lubuntu, but I consistently get the error message: "no file reader exists with source file extension .dat" I realise someone also asked this question before, but I've found no solution to my problem. As it is my .init file and its contents seem to be recognised but the program won't locate/read/accept the .dat file I have in the same location. All that I need the .dat file for is to specify initial Wolbachia infection rates on a patch-by-patch basis. Is there a way to do this in the .init file itself, as if there is I can dispense with the .dat file? Additionally, I am using breed_wolbachia as a LCE, but it doesn't seem to be recognised by the program. When I just input "breed", it is recognised (but the program still stops when it can't find the .dat file). I look forward to hearing from you. I ahve attached my input files, and a copy of the output reading, if it may help in your answering my query. I thank you in advance for any help you're able to give me. Regards Tom Schmidt University of Melbourne |
From: <neh...@lo...> - 2016-04-15 15:15:38
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Hi, My name is Neha Angal, I am a graduate student in biological anthropological. I'm interested in running some simulations of the impacts of drift upon LD during a range expansion. I want to set up linkage block where the haplotype has both neutral and deleterious markers- as in neutral markers surrounding a deleterious marker. I was reading through the manual and it appears that this may be possible? Is there any way to confirm that the markers are occurring in the same linkage block? And is it possible to output the genetic map for each simulation and replicate? Thanks so much! Neha Neha Angal Graduate Research Assistant Masters Student Anthropology Department University of Louisville |