Help infile to migrate-n

[Gisele Dantas]

Dear Peter,

My name is Gisele. I am running "migrate-n" version 3.6.11 on windows. I can not to get migrate read my file. I will tell you all the steps I did, just to check I didn't make any mistake.

I have opened the file using:

I open migrate-n without problem

  =============================================

  MIGRATION RATE AND POPULATION SIZE ESTIMATION

  using Markov Chain Monte Carlo simulation

  =============================================

  PDF output enabled [Letter-size]

  Version 3.4.2   [2065]

  Program started at   Wed Jan 23 08:55:01 2013

  Settings for this run:

  D       Data type currently set to: DNA sequence model            

  I       Input/Output formats

  P       Parameters  [start, migration model]

  S       Search strategy

  W       Write a parmfile

  Q       Quit the program

  To change the settings type the letter for the menu to change

  Start the program with typing Yes or Y

===> 

I typed I, after typed 1 and changed name my file < infilemag >

Dear Peter,

My name is Gisele. I am running "migrate-n" version 3.6.11 on windows. I can not to get migrate read my file. I will tell you all the steps I did, just to check I didn't make any mistake.

I have opened the file using:

I open migrate-n without problem

  =============================================

  MIGRATION RATE AND POPULATION SIZE ESTIMATION

  using Markov Chain Monte Carlo simulation

  =============================================

  PDF output enabled [Letter-size]

  Version 3.4.2   [2065]

  Program started at   Wed Jan 23 08:55:01 2013

  Settings for this run:

  D       Data type currently set to: DNA sequence model            

  I       Input/Output formats

  P       Parameters  [start, migration model]

  S       Search strategy

  W       Write a parmfile

  Q       Quit the program

  To change the settings type the letter for the menu to change

  Start the program with typing Yes or Y

===> 

I typed I, after typed 1 and changed name my file to infilemag 

So, i typed Y to go back main menu.

I typed Y to run, but it cannot read from file infilemag.

I send index my file to see.

Am I doing something wrong?

Gisele Dantas

   

[Peter Beerli]

Dear Gisele,

your file is “infilemag.txt”

if you tell migrate “infilemag.txt” instead only “infilemag” in the menu, then it will work (I guess that on your system you have set the option to hide the file extension)

Peter

<image.png>

So, i typed Y to go back main menu.

<image.png>

I typed Y to run, but it cannot read from file infilemag.

<image.png>

I send index my file to see.

Am I doing something wrong?

Gisele Dantas

   

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<infilemag.txt>

[bruce...@gmail.com]

Dear Gisele,

I have met the same problem when I performed MIGRATE-n on Mac. I also can't use the input file, and even added the ".txt".

I think the problem is that we don't know the default path where the files are.

If we put the input file (for example here "infilemag") to the default file path of MIGRATE-n, it would be solved.

It's occational for me to find the default file path of MIGRATE-n in my Mac. 

After setting the parameters D, I, P, S of the run, I suggest to subsequently set the "W (write the parmfile)", in case you can save your previous settings and use the parmfile later. 

Actually, the path where the new "parmfile" is saved is the default file path of MIGRATE-n! In my Mac, it is "/mac" (the root).

Then put the input file  (for example here "infilemag") to the folder "/mac", then the it successfully run!

So, I think you should find the default file path of MIGRATE-n in your Windows, and then put your input file there. The problem would be solved.

Best,

Bin Ye

在 2017年5月23日星期二 UTC+9上午3:01:50，Gisele Dantas写道：

[Peter Beerli]

the particular problem for @Gisele was number (2) below among some other problems with her runs (see earlier message in this very same stream)

not finding infiles is a really old topic that was discussed now so many times and is mentioned in several places. But it seems it still does need a tutorial.

Here a revisit:

(1) do NOT double click the program icon; use a command line program (Terminal.app on a mac, powershell or command shell or 'cmd run' on windows) 

    then make sure that the migrate binary is executable (that means it is either in the directory were you are you your system knows where

    migrate is or you give the path to migrate, the easiest way for users, who do not want to learn about the details of their operating systems, is

    to place the program in the folder with the data file. But all users should have had a look at a tutorial how to use the commandline environment 

    [google commandline your operating system]

(1a) on macs the default directory is always the home directory (/Users/yourname) on windows the default directory is the directory you 

   are currently in. @bruce I am pretty sure that your advice is faulty: /mac does not exist on most macintosh computers (at least not not mine) and is definitely NOT

   the root directory (this is /) and also is NOT the default directory.

(2) Migrate needs to know the exact name of the inputfile, (some) macs and windows default settings are that they hide the

    file endings .txt .pdf .c etc, in your preferences turn this option off because you want to know all the details. Simply guessing what is the file

    is rather unproductive.

(2a) Migrate has some difficulties on windows to handle path to the infile in the file location recovery feature (the dialog that comes up when 

    migrate cannot find your infile) so simply not using the recovery feature

(3) If you talk about  problems or give advice, let us know not only the _version_ of the migrate but also the version and type of your _operating_ system you run it under!

Peter