error making .bed file using plink

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Manoj Kumar

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Jul 13, 2021, 10:05:43 PM7/13/21
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Hi,
I have hapmap file (.hmp.txt). I am looking to create binary file of this file. Therefore I am using following command but plink shows the following error. please advise.

$plink2 --file se.hmp.txt --make-bed --out se

error:
Error: Unrecognized flag ('--file').

When I try on Linux the plink shows following error:
Error: Failed to open (file_name.hmp.map)

Christopher Chang

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Jul 13, 2021, 10:11:04 PM7/13/21
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Ask the provider of that file what format it's in.  (If it's a single file, it can't possibly be the .ped+.map format that corresponds to --file.)

Manoj Kumar

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Jul 14, 2021, 3:00:10 PM7/14/21
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Hi,
This is hapmap format contains several individuals of a plant species. I am able to run --vcf at plink to make binary file (.bed, bim, .fam) after converting the file in vcf format using tassel. However, I am looking to make these files using the original file in hapmap format. 

Chris Chang

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Jul 14, 2021, 3:23:28 PM7/14/21
to Manoj Kumar, plink2-users
And what would be the point of that?  You already have a tool that converts it into a plink-readable format.  If that’s not good enough for some reason, write the C code yourself and create a pull request if you feel like it; I’m not going to spend my time on a feature only relevant to one person on the planet.

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Manoj Kumar

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Jul 14, 2021, 3:27:06 PM7/14/21
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I know your comments are always rude. I am not posting my issues only for you. 

Manoj Kumar

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Jul 14, 2021, 3:28:51 PM7/14/21
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You are not only the person on the planet who knows everything. 

Chris Chang

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Jul 14, 2021, 3:42:30 PM7/14/21
to Manoj Kumar, plink2-users
Again, the point is that THIS IS NOT AN ISSUE.

Manoj Kumar

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Jul 14, 2021, 3:45:14 PM7/14/21
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WHATEVER, however it seems you know everything.

Chris Chang

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Jul 14, 2021, 3:57:59 PM7/14/21
to Manoj Kumar, plink2-users
It was your responsibility to communicate why this could possibly be an issue.  You did not, and are not, even trying to do that.  The only thing that is clear is that you cannot even be bothered to read the online documentation.

All my work on plink is freely given to the community.  In order for the technical support side of this to be sustainable, I need to meet users halfway: they should engage with the existing documentation and support resources, then I step in (preferably in a way that obviously helps multiple users in the long run) with doc improvements, bugfixes, etc. when they fall short.

You are free to stop using plink if this implicit support contract is not to your liking.

Manoj Kumar

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Jul 14, 2021, 4:11:02 PM7/14/21
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I tried and read the online documents, otherwise how I would run the plink with -vcf file. You are wasting your time and mine too. If you do not want to or do not know just leave this conversation. You always want  to show your intelligency but actually you are not. I was just looking to get an advise about my error that could be a simple solution, I am not an expert on plink.

Chris Chang

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Jul 14, 2021, 4:34:04 PM7/14/21
to Manoj Kumar, plink2-users
Okay, my comment about online documentation was not strictly correct, the initial question about —file is not consistent with a serious attempt to read the docs but yes, you did read something.

However, I stand by the rest of my responses.

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