help running fastsimcoal2

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49ri...@gmail.com

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Jul 5, 2016, 1:41:06 PM7/5/16

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Hello,

I am trying to run fastsimcoal2 with the command ./fsc25 -i 25_25_2.par -n 4 but am receiving this output which seems okay until the bottom (I used ... to save space here).

fastsimcoal was invoked with the following command line arguments:
./fsc25 -i 25_25_2.par -n 4

Random generator seed : 515942

Deme sizes
Deme 0 15000

Sample sizes
Deme 0 4

Sample ages
Deme 0 0

Growth rates
Deme 0 0.6

Historical events
Event 0

#Time : 870
#Source : 0
#Sink : 0
#Migrants : 0
#New size : 1
#New growth rate : -0.1
#New migr. matrix : 0

Event 1

#Time : 970
#Source : 0
#Sink : 0
#Migrants : 0
#New size : 1
#New growth rate : 0.6
#New migr. matrix : 0

Number of independent loci to simulate : 50
Each with a different chromosomal structure

Number of linkage blocks to simulate in structure 1: 2

500 partially linked DNA :
recombination, mutation rates and transition rates :0.0000000000 0.0000000200 0.33000

1 partially linked MICROSAT:
recombination, mutation rates, geometric parameter, and range constraint : 0.0000000000 0.0005000000 0.00000 0

...

Number of linkage blocks to simulate in structure 25: 2

500 partially linked DNA :
recombination, mutation rates and transition rates :0.0000000000 0.0000000200 0.33000

1 partially linked MICROSAT:
recombination, mutation rates, geometric parameter, and range constraint : 0.0000000000 0.0005000000 0.00000 0

Number of linkage blocks to simulate in structure 26: 1

500 partially linked DNA :
recombination, mutation rates and transition rates :0.0000000000 0.0000000200 0.33000

...

Number of linkage blocks to simulate in structure 50: 1

500 partially linked DNA :
recombination, mutation rates and transition rates :0.0000000000 0.0000000200 0.33000

fastsimcoal2 is building 200 genealogies ...

Simulating 50 independent chromosomes using 12 batches and 1 threads.

MRCA time for non-recombining chromosome structure 0: -9223372036854775808
*** Error in `./fsc25': free(): invalid pointer: 0x0000000001b7c5c8 ***
Aborted

These three files are created: 25_25_2_1_1.arp 25_25_2_1.arb 25_25_2_1.simparam
While the .simparam file looks ok, I expected 4 .arp files and them not to be empty.

Does anyone know what is going on?

I have also attached the .par file in a comment.

Thanks in advance.

--Jonathan Rice

49ri...@gmail.com

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Jul 5, 2016, 1:41:26 PM7/5/16

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Here is the .par file
//Number of population samples (demes)
1
//Population effective sizes (number of genes)
15000
//Sample sizes: 2*N
4
//Growth rates : negative growth implies population expansion
0.6
//Number of migration matrices :
0
//historical event: time, source, sink, migrants, new size, new growth rate, mi
2 historical events
970 0 0 0 1 0.6 0
870 0 0 0 1 -0.1 0
//Number of independent loci [chromosome]
50 1
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
2
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
MICROSAT 1 0.0000 0.0005 0 0
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33
//Per chromosome: Number of linkage blocks
1
//per Block: data type, num loci, rec. rate and mut rate + optional parameters
DNA 500 0.00000 0.00000002 0.33

Laurent Excoffier

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Jul 5, 2016, 1:59:59 PM7/5/16

to fastsimcoal

Hi,

the problem is that you have a too large growth rate

2 historical events
970 0 0 0 1 0.6 0
870 0 0 0 1 -0.1 0

Indeed, after 970 generations, your population grows by 60% each generation, so that it quickly exceed the size of storable positive integers, and then the population size becomes negative, triggering the program crash...

Try to better control your max pop size, as your population cannot grow indefinitely backward in time...