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Thread: Tutorial – How to use DIY calculator files and oracle data sheets

  1. #11
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    I also get the "running command 'K.par' had status of 127" message after running the K20 calculator file. However, since I can run the Dodecad Euro 7 par file without issue using the same standardize 23andme format, i.e. copied script from saved file for both K20 & Euro 7 runs so no manual edits, I do not believe in my case that this script is the culprit. This is only my second DIY calculator attempt, however, so I will try a few more for comparison.

    > source('standardize.r')
    > standardize('23andme.txt', company='23andMe')
    > system('K20.par')
    Warning message:
    running command 'K20.par' had status 127
    > system('DIYDodecadWin euro7.par') - This par file worked:
    -----------------------------------------------------------
    -- DIY Dodecad v 2.1 --------------------------------------
    [email protected]@@@@@@----
    -- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
    [email protected]@---
    -- More information: [email protected]@@@@@@----
    ----- Dienekes' Anthropology Blog [email protected]@----------
    -------- http://dienekes.blogspot.com [email protected]@----------
    ----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
    -------- http://dodecad.blogspot.com ----------------------
    -----------------------------------------------------------
    Last edited by AnnieD; 08-01-2015 at 03:13 PM. Reason: clarified par file source

  2. #12
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    I keep getting this error when I try to run the source('standardize.r') I saved all the files in the appropriate folder as shown on step 1 and also changed the directory.

    error in file(filename, "r", encoding = encoding) :
    cannot open the connection
    In addition: Warning message:
    In file(filename, "r", encoding = encoding) :
    cannot open file 'standardize.r': No such file or directory

  3. #13
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    Quote Originally Posted by SWAHILLI_PRINCE16 View Post
    I keep getting this error when I try to run the source('standardize.r') I saved all the files in the appropriate folder as shown on step 1 and also changed the directory.

    error in file(filename, "r", encoding = encoding) :
    cannot open the connection
    In addition: Warning message:
    In file(filename, "r", encoding = encoding) :
    cannot open file 'standardize.r': No such file or directory
    Try loading the R file from the menu, if you are using the RGui program, and not in command prompt. There you can just select the R file you want to load from the menu.

    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




  4. #14
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    Quote Originally Posted by AnnieD View Post
    I also get the "running command 'K.par' had status of 127" message after running the K20 calculator file. However, since I can run the Dodecad Euro 7 par file without issue using the same standardize 23andme format, i.e. copied script from saved file for both K20 & Euro 7 runs so no manual edits, I do not believe in my case that this script is the culprit. This is only my second DIY calculator attempt, however, so I will try a few more for comparison.

    > source('standardize.r')
    > standardize('23andme.txt', company='23andMe')
    > system('K20.par')
    Warning message:
    running command 'K20.par' had status 127
    > system('DIYDodecadWin euro7.par') - This par file worked:
    -----------------------------------------------------------
    -- DIY Dodecad v 2.1 --------------------------------------
    [email protected]@@@@@@----
    -- Copyright (c) 2011 Dienekes Pontikos [email protected]@[email protected]@---
    [email protected]@---
    -- More information: [email protected]@@@@@@----
    ----- Dienekes' Anthropology Blog [email protected]@----------
    -------- http://dienekes.blogspot.com [email protected]@----------
    ----- The Dodecad Ancestry Project [email protected]@@@@@@@@---
    -------- http://dodecad.blogspot.com ----------------------
    -----------------------------------------------------------
    This error happens usually when the par file isn't specifying which chromosomes to read (ie. 1-13 or whatever). (At least in my experience). So the par file reads whole genome and with 23andMe genomes there is MT and Y data. So in that column it doesn't see an integer, like "2", it sees "MT", and it doesn't know what to do because it is expecting an integer value to read.

    What you can do to make it work is after standardizing the file, open "genotype.txt" (this is the standardized output file that will be read by the par file). Click Edit > Find and Replace. Find "MT" Replace "0"; Find "Y", Replace "0"; Find "X", Replace "0". Save. Run the calculator. It should work.
    Last edited by khanabadoshi; 09-26-2016 at 11:34 PM.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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    Quote Originally Posted by khanabadoshi View Post
    Try loading the R file from the menu, if you are using the RGui program, and not in command prompt. There you can just select the R file you want to load from the menu.

    Thanks for the help; I managed to get over the problem I had before however when I try it in this structure

    > source('standardize.r')+
    + standardize('23andMe.txt')=
    + system('DIYDodecadWin euro7.par')

    Error in source("standardize.r") + standardize("23andMe.txt") = system("DIYDodecadWin euro7.par") :
    target of assignment expands to non-language object
    In addition: Warning message:
    running command 'DIYDodecadWin euro7.par' had status 127

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    Quote Originally Posted by SWAHILLI_PRINCE16 View Post
    Thanks for the help; I managed to get over the problem I had before however when I try it in this structure

    > source('standardize.r')+
    + standardize('23andMe.txt')=
    + system('DIYDodecadWin euro7.par')

    Error in source("standardize.r") + standardize("23andMe.txt") = system("DIYDodecadWin euro7.par") :
    target of assignment expands to non-language object
    In addition: Warning message:
    running command 'DIYDodecadWin euro7.par' had status 127
    You have to type it separately.

    > source('standardize.r')
    [Press Enter]

    [Then type]
    >standardize('23andMe.txt')
    [Press Enter and let it run; will take time; no "=" sign]

    [Then type]
    >system('DIYDodecadWin euro7.par')
    [Press Enter; Let it run]
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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  9. #17
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    Quote Originally Posted by khanabadoshi View Post
    This error happens usually when the par file isn't specifying which chromosomes to read (ie. 1-13 or whatever). (At least in my experience). So the par file reads whole genome and with 23andMe genomes there is MT and Y data. So in that column it doesn't see an integer, like "2", it sees "MT", and it doesn't know what to do because it is expecting an integer value to read.

    What you can do to make it work is after standardizing the file, open "genotype.txt" (this is the standardized output file that will be read by the par file). Click Edit > Find and Replace. Find "MT" Replace "0"; Find "Y", Replace "0"; Find "X", Replace "0". Save. Run the calculator. It should work.
    Has this error changed or something. I've tried with my 23&me DNA - doesn't work, same error as AnnieD mentioned. We replace all MTs, Ys, and Xs right?

    Tried brother's FTDNA csv file and get

    Error in file(file, "rt") : cannot open the connection
    In addition: Warning message:
    In file(file, "rt") :

    And father's file, which can open, has the same

    Warning message:
    running command 'K20.par' had status 127

    Error.


    The one Balkan quoted on the first page still works.

  10. #18
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    Quote Originally Posted by FredBats View Post
    Has this error changed or something. I've tried with my 23&me DNA - doesn't work, same error as AnnieD mentioned. We replace all MTs, Ys, and Xs right?

    Tried brother's FTDNA csv file and get

    Error in file(file, "rt") : cannot open the connection
    In addition: Warning message:
    In file(file, "rt") :

    And father's file, which can open, has the same

    Warning message:
    running command 'K20.par' had status 127

    Error.


    The one Balkan quoted on the first page still works.

    This must be something different. The MT/Y DNA error doesn't happen with FTDNA data because the raw files only have autosomal data, no MT/Y data.


    Which calculator are you trying to run? I can try running it for you.


    EDIT: I was incorrect. Status 127 doesn't have anything with the integers -- that is another error.
    Status 127 means that the PAR file or DIYDODECADWIN is not on the PATH, and thus, not visible to R to use. Most likely, the PAR file and DIYDODECADWIN.EXE files aren't in the same directory and/or that directory isn't the set Working Directory?

    http://stackoverflow.com/questions/3...urns-error-127
    http://stackoverflow.com/questions/2...had-status-127
    http://stackoverflow.com/questions/3...not-on-windows

    According to the last link, if the path C:/DIY or whatever has a [space] in it, it can lead to a Status 127. ie. C:/Khana/DIY FILES/k20.par -- maybe changing the folder name to DIY_FILES [C:/Khana/DIY_Files/k20.par] will solve this issue.
    Last edited by khanabadoshi; 10-26-2016 at 08:12 AM.
    “Chahar chez est tohfay Multan, Gard-o- Garma, Gada-o- Goristan”.

    Four things are the gift of Multan: Dusty winds, hot seasons, beggars and graveyards.




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  12. #19
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    Quote Originally Posted by khanabadoshi View Post
    Which calculator are you trying to run? I can try running it for you.
    If it comes to that sure. Got it to work last night - tried it before work today and the silly thing continually reset to the "start" no standardize.r when trying to continue with entering my 23&me information.

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    Eurogenes K36 DIY calculator files:

    https://onedrive.live.com/?authkey=%...&action=locate

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