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From: Vasili <vas...@gm...> - 2019-10-16 13:22:55
|
Dear SFS_code users,
I was trying to simulate a locus under negative selection within a
neutrality evolving region in a way, similar to the one from Torres et al.,
2018. Ultimately I want to go for a 2.2 Mb region, but to start with I'm
using a 100x shorter region. My command is as follows (I'm using the
sfs_code version from the aforementioned paper as I want to draw values for
the selection coefficient from two negative gamma distributions):
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code 1 1 \
-r 6.0443e-05 -N 18449 -s 111 -n 100 \
-TE 0.5994242 \
-Td 0 2.10709 -Td 0.437017 0.152957396219 -Td 0.546498 0.573964845871 -Tg
0.546498 60.0453856768 \
-t 0.000861 \
-L 11 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 \
-v L A 2000 -v L 5 409 \
-W 0 -W L 5 2 -0.3394 0.184 0.00040244 0.0415 0.00515625 \
-a N \
-o 2000test.txt
when running it I get an output that ends with a mutation in the 7th locus
7,A,1959,-14141,22117,GTG,G,0,X,X,0.0,156,0.0,0.2,0.3,0.4,0.8,0.9,0.10,0.12,0.13,0.14,0.16,0.18,0.19,0.20,0.21,0.22,0.24,0.25,0.26,0.27,0.28,0.29,0.31,0.32,0.33,0.34,0.35,0.37,0.38,0.39,0.40,0.42,0.43,0.44,0.47,0.49,0.51,0.53,0.54,0.55,0.56,0.57,0.58,0.59,0.60,0.61,0.62,0.63,0.64,0.66,0.68,0.71,0.72,0.73,0.74,0.75,0.76,0.77,0.78,0.79,0.80,0.81,0.82,0.83,0.84,0.85,0.86,0.87,0.88,0.89,0.90,0.91,0.93,0.94,0.95,0.97,0.100,0.101,0.102,0.103,0.104,0.106,0.107,0.108,0.109,0.111,0.113,0.114,0.115,0.116,0.117,0.118,0.119,0.120,0.121,0.122,0.123,0.124,0.125,0.127,0.128,0.130,0.131,0.132,0.133,0.134,0.135,0.136,0.137,0.139,0.140,0.141,0.144,0.145,0.146,0.147,0.149,0.150,0.151,0.152,0.153,0.154,0.155,0.156,0.159,0.160,0.161,0.162,0.163,0.164,0.166,0.167,0.168,0.169,0.172,0.173,0.174,0.175,0.176,0.177,0.178,0.179,0.182,0.183,0.184,0.185,0.186,0.187,0.190,0.191,0.192,0.193,0.195,0.196,0.197,0.199;
so for some reason, it stops at the 8th locus, which isn't special in any
way
Below is the error I'm getting:
*** Error in
`/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code': free():
invalid next size (fast): 0x00000000010052a0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81489)[0x2ab6717bf489]
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code[0x4025d8]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ab6717603d5]
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code[0x40348f]
======= Memory map: ========
00400000-0047a000 r-xp 00000000 00:2b 68985308
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code
00679000-0067a000 r--p 00079000 00:2b 68985308
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code
0067a000-0067b000 rw-p 0007a000 00:2b 68985308
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code
01004000-03531000 rw-p 00000000 00:00 0
[heap]
2ab671218000-2ab67123a000 r-xp 00000000 fd:01 201895039
/usr/lib64/ld-2.17.so
2ab67123a000-2ab67123e000 rw-p 00000000 00:00 0
2ab671249000-2ab67124c000 rw-p 00000000 00:00 0
2ab671371000-2ab671395000 rw-p 00000000 00:00 0
2ab6713b1000-2ab6713e2000 rw-p 00000000 00:00 0
2ab6713f8000-2ab67141f000 rw-p 00000000 00:00 0
2ab671439000-2ab67143a000 r--p 00021000 fd:01 201895039
/usr/lib64/ld-2.17.so
2ab67143a000-2ab67143b000 rw-p 00022000 fd:01 201895039
/usr/lib64/ld-2.17.so
2ab67143b000-2ab67143c000 rw-p 00000000 00:00 0
2ab67143c000-2ab67153d000 r-xp 00000000 fd:01 201340513
/usr/lib64/libm-2.17.so
2ab67153d000-2ab67173c000 ---p 00101000 fd:01 201340513
/usr/lib64/libm-2.17.so
2ab67173c000-2ab67173d000 r--p 00100000 fd:01 201340513
/usr/lib64/libm-2.17.so
2ab67173d000-2ab67173e000 rw-p 00101000 fd:01 201340513
/usr/lib64/libm-2.17.so
2ab67173e000-2ab671900000 r-xp 00000000 fd:01 201328540
/usr/lib64/libc-2.17.so
2ab671900000-2ab671b00000 ---p 001c2000 fd:01 201328540
/usr/lib64/libc-2.17.so
2ab671b00000-2ab671b04000 r--p 001c2000 fd:01 201328540
/usr/lib64/libc-2.17.so
2ab671b04000-2ab671b06000 rw-p 001c6000 fd:01 201328540
/usr/lib64/libc-2.17.so
2ab671b06000-2ab671b2d000 rw-p 00000000 00:00 0
2ab671b4f000-2ab671b93000 rw-p 00000000 00:00 0
2ab671ba9000-2ab671bed000 rw-p 00000000 00:00 0
2ab671bed000-2ab671c31000 rw-p 00000000 00:00 0
2ab671c38000-2ab671c7c000 rw-p 00000000 00:00 0
2ab671c89000-2ab671cba000 rw-p 00000000 00:00 0
2ab671cd2000-2ab671cf6000 rw-p 00000000 00:00 0
2ab671cf6000-2ab671d19000 rw-p 00000000 00:00 0
2ab671d37000-2ab671d7b000 rw-p 00000000 00:00 0
2ab671dd1000-2ab671e15000 rw-p 00000000 00:00 0
2ab671e15000-2ab671e2a000 r-xp 00000000 fd:01 201794459
/usr/lib64/libgcc_s-4.8.5-20150702.so.1
2ab671e2a000-2ab672029000 ---p 00015000 fd:01 201794459
/usr/lib64/libgcc_s-4.8.5-20150702.so.1
2ab672029000-2ab67202a000 r--p 00014000 fd:01 201794459
/usr/lib64/libgcc_s-4.8.5-20150702.so.1
2ab67202a000-2ab67202b000 rw-p 00015000 fd:01 201794459
/usr/lib64/libgcc_s-4.8.5-20150702.so.1
2ab674000000-2ab674021000 rw-p 00000000 00:00 0
2ab674021000-2ab678000000 ---p 00000000 00:00 0
7fff17b6a000-7fff17b8b000 rw-p 00000000 00:00 0
[stack]
7fff17bd1000-7fff17bd3000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
/var/spool/slurm/slurmd/job08874/slurm_script: line 22: 4934 Aborted
(core dumped)
/mmg/vasili85/SFS_code/SFS_CODE_torres_et_al_2018/bin/sfs_code 1 1 -r
6.0443e-05 -N 18449 -s 111 -n 100 -TE 0.5994242 -Td 0 2.10709 -Td 0.437017
0.152957396219 -Td 0.546498 0.573964845871 -Tg 0.546498 60.0453856768 -t
0.000861 -L 11 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 2000 -v L
A 2000 -v L 5 409 -W 0 -W L 5 2 -0.3394 0.184 0.00040244 0.0415 0.00515625
-a N -o 2000test.txt
I've tried different random seeds and allocating up to 80g of RAM (some
desperate moves).
Most likely I'm doing something obviously wrong, but I can't see whether
the problem lies. And yes, that's my first experience with sfs_code and
forward simulators in general.
Would greatly appreciate any hint.
Kind regards,
Vasili
<https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail>
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вирусов. www.avast.ru
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|
|
From: 唐亮 <tan...@ha...> - 2016-10-05 14:50:46
|
Hill everyone, I'm a novice to SFS_CODE. I have a basic question, when the simulated species has the gametophytic self-incompatibility (GSI) system (e.g. P1: S1S2 X P2 S2S3, under GSI, the offsprings would be S1S3 or S2S3). In such case, how should I choose the parameter value to account for GSI and do simulation? Thank you all very much! Sincerely Liang Tang |
|
From: Florian C. <flo...@gm...> - 2016-03-06 08:40:20
|
Hi, I would like to simulate a selective sweep in a time series experiment, i.e. with a sample of the allele frequencies before and after the sweep. First I simulated the desired selective sweep pattern without considering time series data using following command: ./sfs_code 1 1 -t 0.01 -r 0.05 -n 25 -L 1 10000 -a N --mutation 0 S 5000 G 1000 --trackTrajectory S 5000 R 1 1 A G 0 -TE 3 Then I tried to create time series data by copying the ancestral population at time 0 and immediately stopping the simulation for this copy (keeping the rest of the command as it was for the sweep): ./sfs_code 2 1 -TS 0 0 1 -TE 0 0 -t 0.01 -r 0.05 -n 25 -L 1 10000 -a N --mutation 0 P 1 S 5000 G 1000 --trackTrajectory S 5000 R 1 1 A G 0 -TE 3 The problem is that these simulations ran for days (compared to minutes in the case without time series data) and did not produce the expected sweep pattern. If anyone has an idea on this, I'd be grateful to get some advice. Best wishes, Florian |
|
From: Rémi Matthey-D. <ma...@zo...> - 2016-02-29 21:40:10
|
Hi all, *Goal* I am trying to simulate 3 unlinked *groups* of 5 linked *loci *each (for a total of 15 loci). Cross-overs occur within each group and its rate varies from group to group. Annotation (coding/non-coding and selection coefficients) varies from locus to locus. *Why I am getting confused* I can indicate the genetic distance between loci with *--linkage. *However, when annotating with a file (*-a F annotate.txt*), one must indicate the physical distance, which entries will, I suppose, play out with the map file (*-r F map.txt*) in order to calculate the genetic distance. If this is true it means that the *--linkage* command is then ignored. If I understand correctly using *-a F annotate.txt *necessarily causes SFS_CODE to not consider *--linkage*. Now, the issue is that in the map file (*-r F map.txt*), I think it is impossible to indicate several unlinked loci. *Question* Can you help me with that by sending me a minimalist code line and file example that would make the simulation I am trying to have? Thanks a lot for your help. Remi -- Remi Matthey-Doret www.zoology.ubc.ca/~matthey/ PhD Candidate, M. Whitlock Lab Beaty Biodiversity Research Center, room 250 Dept. of Zoology, University of British Columbia 6270 University Blvd, Vancouver, BC, V6T 1Z4 @RemiMD Phone: (604) 369-5929 |
|
From: Daniel R. <dr...@sa...> - 2015-11-19 14:56:35
|
Hi, I have stumbled across a memory corruption error when running convertSFS_CODE: *** glibc detected *** /nfs/team143/software/sfs_code/bin/convertSFS_CODE: malloc(): memory corruption: 0x0000000000fda470 *** The command used to generate the simulation output is: sfs_code 1 100 -N 7000 -n 5000 -A -L 1 5000 -t 0.001 -r 0.001 -TW 0 P 0 1 140.0 0 1 -Td 0.265753 P 0 0.128575 -Td 0.342466 P 0 0.554541 -Tg 0.342466 P 0 44.822 -Tg 0.391465 P 0 284.7 -TW 0.391465 P 0 1 140.0 0 1 -TE 0.405479 --seed 22732920 --outfile small.test.o --popFreq small.test.freq The command used in the attempt to generate the SFS is: convertSFS_CODE small.test.o --SFS > small.test.sfs I have created a repository https://github.com/dlrice/sfs_coder_small_test that contains the following files to recreate the error: * Command used to create the simulation is located in small.test.sh. * Output is located in small.test.o * Frequency output is located in small.test.freq * convertSFS_CODE command is located in to_sfs.sh * VERSION contains the version of sfs_code / convertSFS_CODE The converstSFS_CODE binary has worked in the past, it just seems to struggle with this particular simulation. Any advice would be appreciated. Cheers, Dan -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
|
From: Clement K. <cle...@gm...> - 2015-11-03 13:16:57
|
That -fast was not a recognized compiler directive On Tue, Nov 3, 2015 at 2:00 AM, Ryan Hernandez <rh...@gm...> wrote: > Hi Clement, > > What warnings did you get? > > Ryan > > > On Mon, Nov 2, 2015 at 1:14 PM, Clement Kent <cle...@gm...> > wrote: > >> Hi - installing sfs_code on a Mac OS X Yosemite 10.10.5, I edited -03 to >> -fast in the makefile, as suggested in the manual (last paragraph of >> section 3.2). This produced warning message during make. >> >> I checked my gcc options, and changed the -fast to -ffast-math in the >> makefile; after this change, make ran cleanly. >> >> Cheers, >> Clement Kent >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> sfscode-users mailing list >> sfs...@li... >> https://lists.sourceforge.net/lists/listinfo/sfscode-users >> >> > |
|
From: Ryan H. <rh...@gm...> - 2015-11-03 07:00:36
|
Hi Clement, What warnings did you get? Ryan On Mon, Nov 2, 2015 at 1:14 PM, Clement Kent <cle...@gm...> wrote: > Hi - installing sfs_code on a Mac OS X Yosemite 10.10.5, I edited -03 to > -fast in the makefile, as suggested in the manual (last paragraph of > section 3.2). This produced warning message during make. > > I checked my gcc options, and changed the -fast to -ffast-math in the > makefile; after this change, make ran cleanly. > > Cheers, > Clement Kent > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
|
From: Clement K. <cle...@gm...> - 2015-11-02 21:14:44
|
Hi - installing sfs_code on a Mac OS X Yosemite 10.10.5, I edited -03 to -fast in the makefile, as suggested in the manual (last paragraph of section 3.2). This produced warning message during make. I checked my gcc options, and changed the -fast to -ffast-math in the makefile; after this change, make ran cleanly. Cheers, Clement Kent |
|
From: Paula T. <pa...@cs...> - 2015-10-21 12:37:00
|
Hi,
I am using SFS_CODE for simulating data that undergoes a complex demographic scenario. In the end I want to compare the parameters I used in the simulation with some estimates. In my estimates, I have everything scaled by Ne. It seems to me though that the parameters in SFS_CODE are scaled by Na (the ancestral population size, the one used in the burn-in period and specified with -N).
The documentation seems a bit ambiguous about the scaling, but, for example, it says that theta is scaled by Ne (page 7). However, looking at the code, it seems that theta and selection parameters are all updated when the population size is changed. I found the following code lines (line 2500, version 20150815):
ppars[pop].Nt *= foo;
ppars[pop].THETA *= foo;
ppars[pop].INSRATE *= foo;
ppars[pop].DELRATE *= foo;
if(ppars[pop].RHO > DBL_MIN)
ppars[pop].RHO *= foo;
else if(ppars[pop].fGC > DBL_MIN)
ppars[pop].fGC *= foo;
for(r=0; r<gpars.R; r++){
ppars[pop].GAMMA[r] *= foo;
ppars[pop].lambdaN[r] /= foo;
ppars[pop].lambdaP[r] /= foo;
ppars[pop].normMean[r] *= foo;
ppars[pop].normVar[r] *= (foo*foo);
which, seems to me, means that all parameters (at the input) are in fact scaled by Na and not Ne.
Is this correct or am I missing something?
I think it would be very useful if this was explained in the documentation more clearly. It would also be nice to be able to obtain an Ne (using convertSFS_CODE, for example) from a run with a given demography.
Thank you.
Best regards,
Paula Tataru
--------------------------------------------
Bioinformatics Research Centre,
Aarhus University,
Denmark
|
|
From: Paula T. <pa...@cs...> - 2015-10-21 12:33:07
|
Hi,
I am using SFS_CODE for simulating data that undergoes a complex demographic scenario. In the end I want to compare the parameters I used in the simulation with some estimates. In my estimates, I have everything scaled by Ne. It seems to me though that the parameters in SFS_CODE are scaled by Na (the ancestral population size, the one used in the burn-in period and specified with -N).
The documentation seems a bit ambiguous about the scaling, but, for example, it says that theta is scaled by Ne (page 7). However, looking at the code, it seems that theta and selection parameters are all updated when the population size is changed. I found the following code lines (line 2500, version 20150815):
ppars[pop].Nt *= foo;
ppars[pop].THETA *= foo;
ppars[pop].INSRATE *= foo;
ppars[pop].DELRATE *= foo;
if(ppars[pop].RHO > DBL_MIN)
ppars[pop].RHO *= foo;
else if(ppars[pop].fGC > DBL_MIN)
ppars[pop].fGC *= foo;
for(r=0; r<gpars.R; r++){
ppars[pop].GAMMA[r] *= foo;
ppars[pop].lambdaN[r] /= foo;
ppars[pop].lambdaP[r] /= foo;
ppars[pop].normMean[r] *= foo;
ppars[pop].normVar[r] *= (foo*foo);
which, seems to me, means that all parameters (at the input) are in fact scaled by Na and not Ne.
Is this correct or am I missing something?
I think it would be very useful if this was explained in the documentation more clearly. It would also be nice to be able to obtain an Ne (using convertSFS_CODE, for example) from a run with a given demography.
Thank you.
Best regards,
Paula Tataru
--------------------------------------------
Bioinformatics Research Centre,
Aarhus University,
Denmark
|
|
From: Daniel R. <dr...@sa...> - 2015-10-19 16:14:58
|
Hi, First of all, thanks a lot for writing SFS_CODE and for providing excellent documentation. I'm attempting to recreate some figures from Zuk et al.'s Searching for missing heritability: Designing rare variant association studies with SFS_CODE. Figures 1 (B) & (C), seen at ( http://www.pnas.org/content/111/4/E455/F1.expansion.html ) are the individual allele frequencies for equillibrium and European populations. I would like to sample the entire population in SFS_CODE to count the allele frequencies and noticed that in the documentation we can do this with the option --sampSize and from Table 6 on p57 of August 15, 2015 it has Sample <SS1> individuals from population 1, ..., <SSNPOP> individuals from population NPOP. Use the value -1 to sample an entire population. (p??) I have attempted to grab all samples in the population with the -1 option as follows (note that I am only performing one iteration and using a small population size to for quick testing purposes): $ sfs_code 1 1 --popSize 1000 --additive --length 1 1500 --substMod 0 --theta 0.034 --selDistType 1 2.91587694999271 0 1 -TE 0 --printGen --sampSize -1 --ploidy 2 > not enough arguments after --sampSize (entry 22) > For usage type: sfs_code -h<return> Then I have tried to indicate the population index: $ sfs_code ... --sampSize 1 -1 > my apologies. -1 has not been implemented. > For usage type: sfs_code -h<return> In my example it's not a big deal as the population doesn't grow but in Zuk there is some exponential population growth, which I can approximate if need be - I just wanted to check to see if there was something simple I'm doing wrong. Cheers, Dan -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
|
From: Tatum M. <tmo...@wi...> - 2015-09-15 14:49:16
|
Hi Ryan, For the simulation with gene conversion: sfs_code 1 5 -t 0.0014 -L 1 2516575 -H 0.00063 1549 -P 1 -n 13 -Td 0 4 -TE 0.03 For the simulation without gene conversion: sfs_code 1 5 -t 0.0015 -L 1 4411532 -P 1 -n 200 -Td 0 25 -TE 0.051 I could use the exact same parameters with and without gene conversion if that would be helpful. I had already done these simulations, so they were easy to look at. Tatum On Mon, Sep 14, 2015 at 6:55 PM Ryan Hernandez <rh...@gm...> wrote: > Hi Tatum, > > Can you remind me what parameters you are using for the two sets of > simulations you mention here? > > Thanks, > > Ryan > > On Mon, Sep 14, 2015 at 3:20 PM, Tatum Mortimer <tmo...@wi...> > wrote: > >> Hi Ryan, >> >> This reply is regarding a previous question about simulating bacterial >> recombination. I wasn't a member of the mailing list then, and I can't >> figure out how to respond to that message specifically. I've recently been >> using SFS_CODE to simulate bacterial populations, including gene >> conversion. When I run a recombination detection program (BRATNextGen) on >> the results of the simulation, tracts of similar size to my input on the >> command line are detected. I also double checked this by running a strictly >> clonal simulation, and BRATNextGen detected no recombination. In your >> previous answer, you said that gene conversion only works in diploids and >> tetraploids. However, it appears that gene conversion is occurring in my >> haploid simulations. >> >> Best, >> Tatum >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> sfscode-users mailing list >> sfs...@li... >> https://lists.sourceforge.net/lists/listinfo/sfscode-users >> >> > |
|
From: Louise M. <lhm...@gm...> - 2015-09-15 13:55:10
|
perfect, thanks so much! On Mon, Sep 14, 2015 at 5:02 PM, Ryan Hernandez <rh...@gm...> wrote: > Helo Louise, > > Yes, it is possible. You should see the --rateClassLoci option in the > documentation. You would specify the overall theta/site that you want to > use, and then can modify the relative rate of each locus using this > command. E.g., to have locus 0 have a 10-fold increase rate above > background you would add -v L 0 10. > > R > > > > On Mon, Sep 14, 2015 at 2:02 PM, Louise Moncla <lhm...@gm...> wrote: > >> Hello, >> >> I am using SFS_CODE to simulate 8 unlinked loci and am wondering if it is >> possible to specify a different theta value for each locus. >> >> Thanks! >> >> ~ Louise >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> sfscode-users mailing list >> sfs...@li... >> https://lists.sourceforge.net/lists/listinfo/sfscode-users >> >> > |
|
From: Ryan H. <rh...@gm...> - 2015-09-14 23:55:01
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Hi Tatum, Can you remind me what parameters you are using for the two sets of simulations you mention here? Thanks, Ryan On Mon, Sep 14, 2015 at 3:20 PM, Tatum Mortimer <tmo...@wi...> wrote: > Hi Ryan, > > This reply is regarding a previous question about simulating bacterial > recombination. I wasn't a member of the mailing list then, and I can't > figure out how to respond to that message specifically. I've recently been > using SFS_CODE to simulate bacterial populations, including gene > conversion. When I run a recombination detection program (BRATNextGen) on > the results of the simulation, tracts of similar size to my input on the > command line are detected. I also double checked this by running a strictly > clonal simulation, and BRATNextGen detected no recombination. In your > previous answer, you said that gene conversion only works in diploids and > tetraploids. However, it appears that gene conversion is occurring in my > haploid simulations. > > Best, > Tatum > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
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From: Tatum M. <tmo...@wi...> - 2015-09-14 22:20:27
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Hi Ryan, This reply is regarding a previous question about simulating bacterial recombination. I wasn't a member of the mailing list then, and I can't figure out how to respond to that message specifically. I've recently been using SFS_CODE to simulate bacterial populations, including gene conversion. When I run a recombination detection program (BRATNextGen) on the results of the simulation, tracts of similar size to my input on the command line are detected. I also double checked this by running a strictly clonal simulation, and BRATNextGen detected no recombination. In your previous answer, you said that gene conversion only works in diploids and tetraploids. However, it appears that gene conversion is occurring in my haploid simulations. Best, Tatum |
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From: Ryan H. <rh...@gm...> - 2015-09-14 22:02:50
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Helo Louise, Yes, it is possible. You should see the --rateClassLoci option in the documentation. You would specify the overall theta/site that you want to use, and then can modify the relative rate of each locus using this command. E.g., to have locus 0 have a 10-fold increase rate above background you would add -v L 0 10. R On Mon, Sep 14, 2015 at 2:02 PM, Louise Moncla <lhm...@gm...> wrote: > Hello, > > I am using SFS_CODE to simulate 8 unlinked loci and am wondering if it is > possible to specify a different theta value for each locus. > > Thanks! > > ~ Louise > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
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From: Louise M. <lhm...@gm...> - 2015-09-14 21:03:05
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Hello, I am using SFS_CODE to simulate 8 unlinked loci and am wondering if it is possible to specify a different theta value for each locus. Thanks! ~ Louise |
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From: Ryan H. <rh...@gm...> - 2015-09-11 06:28:44
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Hi Yang, You could use something like this: ./sfs_code 1 1 -L 1 10000 -a N --mutation 0 S 5000 G 1000 --trackTrajectory S 5000 R 1 1 A G 0 -TE 3 This will generate a single locus of length 10kb that is non-coding, introduce a mutation just after the burn-in at position 5kb with strong selection coefficient gamma=2Ns=1000, then use the --trackTrajectory option to follow this particular site until it fixes (R 1 1) automatically restarting if it is lost by drift (A), and stop the simulation right after fixation (G 0). The -TE 3 is there to keep SFS_CODE running until fixation. The value of 3 is just an arbitrarily large number (relative to expected fixation time) that might as well be 1000. This seems to be necessary, and is kind of a bug that I will fix in the next release. Hope this helps. Let me know if you have questions. R On Thu, Sep 10, 2015 at 10:04 PM, Young <dre...@gm...> wrote: > Dear Ryan and SFS_CODE'ers, > > I have a basic question about SFS_CODE. I want to simulate a selective > sweep event in a model as following. One segment of sequence of length > 10000bp under the infinite-site model, and at some time a beneficial allele > appeared at the midpoint of the sequence, and finally the sample is > collected at the time of fixation or shortly after the fixation. All the > mutations should be neutral. It would be appreciated if you could provide > me the SFS_CODE command line that can simulate such a selective sweep. I > have read the manual but still not very clear about this. > > Best regards, > Yang > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
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From: Young <dre...@gm...> - 2015-09-11 05:04:39
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Dear Ryan and SFS_CODE'ers, I have a basic question about SFS_CODE. I want to simulate a selective sweep event in a model as following. One segment of sequence of length 10000bp under the infinite-site model, and at some time a beneficial allele appeared at the midpoint of the sequence, and finally the sample is collected at the time of fixation or shortly after the fixation. All the mutations should be neutral. It would be appreciated if you could provide me the SFS_CODE command line that can simulate such a selective sweep. I have read the manual but still not very clear about this. Best regards, Yang |
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From: Ryan H. <rh...@gm...> - 2015-09-10 19:54:42
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Hi SFS_CODE'ers, I've posted a slightly updated version of SFS_CODE that fixes a bug that was pointed out by Marguerite Lapierre. She found that when simulating haploid populations, the mutation rate was 2-fold too large. This bug also impacted tetraploid simulations. Diploid simulations were not affected by this bug. Feel free to download the latest version: https://sourceforge.net/projects/sfscode/files/sfscode/sfscode_20150910/. Happy simulating, Ryan |
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From: Ryan H. <rh...@gm...> - 2015-09-03 21:27:17
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Hi Brian, No, gene conversion only works with diploids and tetraploids. Sorry! Ryan On Thu, Sep 3, 2015 at 8:09 AM, Brian Arnold <bri...@gm...> wrote: > Hello, > > I would like to potentially simulate bacterial recombination with > selection. Does SFS code allow the use of gene conversion with the haploid > model, which would effectively simulate recombination in haploids? > > Thanks! > Brian Arnold > > > > ------------------------------------------------------------------------------ > Monitor Your Dynamic Infrastructure at Any Scale With Datadog! > Get real-time metrics from all of your servers, apps and tools > in one place. > SourceForge users - Click here to start your Free Trial of Datadog now! > http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
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From: Brian A. <bri...@gm...> - 2015-09-03 15:09:37
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Hello, I would like to potentially simulate bacterial recombination with selection. Does SFS code allow the use of gene conversion with the haploid model, which would effectively simulate recombination in haploids? Thanks! Brian Arnold |
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From: Shujun O. <ous...@ms...> - 2014-11-23 16:32:09
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Hi Ryan,
I want to convert the SFS_CODE result to fasta and SFS by using
convertSFS_CODE and I received the following error msg:
./convertSFS_CODE test4.td3selfN2kL5k5.sim -s F
test4.td3selfN2kL5k5.sfs -a F test4.td3selfN2kL5k5.fa
converSFS_CODE error: did not read Nc correctly on line 13
I am using the 2014-07-20 version, and the command line:
./sfs_code 4 1 -t 0.003 -N 2000 -r 0.00032 -L 5 5000 -i 0.2 -Ti 0
0.99 -n 50 -w 0 -TD 0 0 1 0.05 1500 -Tw 1 1 -TD 1 0 2 0.05 1500 -Tw 2 2 -TD
2 0 3 0.05 1500 -Tw 3 3 -TE 3 -o test4.td3selfN2kL5k5.sim
in order to simulate time dependent domestication events.
I have attached the output file in this email. If you found any irrational
setting in my command, please point it out. Thank you very much!
Regards,
Shujun
_________________---------_____________
Shujun Ou
PhD Graduate Research Assistant
Department of Horticulture
Michigan State University
Plant & Soil Sciences Building, Rm A334
East Lansing, MI 48824
Phone: (517) 355-5191 x 1383
Email: ous...@ms... <mailto:%20o...@ms...>
http://www.hrt.msu.edu/shujun-ou
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From: Ryan H. <rh...@gm...> - 2014-11-01 04:27:46
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Hi Shujun, No, not exactly. The rate that you want to enter is rho=4*Ne*r. In this case, the r is equivalent to Morgans per base. And then you will need an estimate of the effective population size, Ne. Please let me know if you have other questions. Best, Ryan On Fri, Oct 31, 2014 at 2:25 PM, Shujun Ou <ous...@ms...> wrote: > Hi, > > > > I have a quick question. If the recombination rate I want to study is > 4cM/Mb, should I set the -r parameter 4? > > > > Thanks, > > > > Shujun > > > > ______________________________ > > Shujun Ou > > PhD Graduate Research Assistant > > Department of Horticulture > > Michigan State University > > Plant & Soil Sciences Building, Rm A334 > > East Lansing, MI 48824 > > Phone: (517) 355-5191 x 1383 > > Email: ous...@ms... <%20o...@ms...> > > http://www.hrt.msu.edu/shujun-ou > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sfscode-users mailing list > sfs...@li... > https://lists.sourceforge.net/lists/listinfo/sfscode-users > > |
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From: Shujun O. <ous...@ms...> - 2014-10-31 22:27:39
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Hi, I have a quick question. If the recombination rate I want to study is 4cM/Mb, should I set the -r parameter 4? Thanks, Shujun _________________---------_____________ Shujun Ou PhD Graduate Research Assistant Department of Horticulture Michigan State University Plant & Soil Sciences Building, Rm A334 East Lansing, MI 48824 Phone: (517) 355-5191 x 1383 Email: ous...@ms... <mailto:%20o...@ms...> http://www.hrt.msu.edu/shujun-ou |
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