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syntheke / bayesR

Bayesian hierarchical model for complex trait analysis
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Format/Readme file issue #2

Closed nicolazzie closed 6 years ago

nicolazzie commented 9 years ago

Hi, first of all, thanks for your bayesR model. I'm starting heavy testing on simulated (WGS) data... and I've encountered a couple of issues:

1) Line 60: write(21,903) 'SNP output ', snpout Format 903 for snpout is i8, whereas snpout is logical. When running the pgm I get: 

At line 60 of file bayesR.f90 (unit = 21, file = 'simout.log')
Fortran runtime error: Expected INTEGER for item 3 in formatted transfer, got LOGICAL
(a,t30,'= ',i8)
            ^

I've patched it locally by adding a new format and editing line 60 as below.

2) The readme file should be edited

The command line provided: bayesR -bfile simdata -out simout -numit 10000 -burnin 5000 -seed 333 does not work when running the example provided. It should be changed to: bayesR -bfile example/simle -out simout -numit 10000 -burnin 5000 -seed 333

simout.log file now looks like this:

Program BayesR
      Run started at 2015-01-30 09:34:47
Prefix for input files       : example/simle
Prefix for output files      : simout
Phenotype column             =        1
No. of loci                  =    20000
No. of individuals           =     1000
No. of training individuals  =     1000
Prior Vara                   =   0.010000 -2.000000
Prior Vare                   =   0.010000 -2.000000
Model size                   =        0
No. of cycles                =      100
Burnin                       =       50
Thinning rate                =       10
No. of mixtures              =        4
Variance of dist             =    0.00000   0.00010   0.00100   0.01000
Dirichlet prior              =    1.00000   1.00000   1.00000   1.00000
Seed                         =      333
SNP output                   = F

Again, thank you for your work. We will be testing it intensively in the next few weeks. Best regards, E. Nicolazzi

syntheke commented 9 years ago

Hi Ezequiel

Thanks for spotting this, I will look into it. THE code we put in the public domain is an last hour re-write to make the programs more user friendly. Most likely there will be a few more mistakes.

Cheers

Gerhard

Gerhard Moser The University of Queensland Queensland Brain Institute (QBI) QBI Building (#79) St Lucia, QLD 4072 Australia Phone: +61 7 3346 6429

From: Ezequiel Luis Nicolazzi notifications@github.com<mailto:notifications@github.com> Reply-To: syntheke/bayesR reply@reply.github.com<mailto:reply@reply.github.com> Date: Friday, 30 January 2015 6:54 PM To: syntheke/bayesR bayesR@noreply.github.com<mailto:bayesR@noreply.github.com> Subject: [bayesR] Format/Readme file issue (#2)

Hi, first of all, thanks for your bayesR model. I'm starting heavy testing on simulated (WGS) data... and I've encountered a couple of issues:

1) Line 60: write(21,903) 'SNP output ', snpout Format 903 for snpout is i8, whereas snpout is logical. When running the pgm I get:

At line 60 of file bayesR.f90 (unit = 21, file = 'simout.log') Fortran runtime error: Expected INTEGER for item 3 in formatted transfer, got LOGICAL (a,t30,'= ',i8) ^

I've patched it locally by adding a new format and editing line 60 as below.

2) The readme file should be edited

The command line provided: bayesR -bfile simdata -out simout -numit 10000 -burnin 5000 -seed 333 does not work when running the example provided. It should be changed to: bayesR -bfile example/simle -out simout -numit 10000 -burnin 5000 -seed 333

simout.log file now looks like this:

Program BayesR Run started at 2015-01-30 09:34:47 Prefix for input files : example/simle Prefix for output files : simout Phenotype column = 1 No. of loci = 20000 No. of individuals = 1000 No. of training individuals = 1000 Prior Vara = 0.010000 -2.000000 Prior Vare = 0.010000 -2.000000 Model size = 0 No. of cycles = 100 Burnin = 50 Thinning rate = 10 No. of mixtures = 4 Variance of dist = 0.00000 0.00010 0.00100 0.01000 Dirichlet prior = 1.00000 1.00000 1.00000 1.00000 Seed = 333 SNP output = F

Again, thank you for your work. We will be testing it intensively in the next few weeks. Best regards, E. Nicolazzi

— Reply to this email directly or view it on GitHubhttps://github.com/syntheke/bayesR/issues/2.