error: C compiler cannot create executables while installing fastStrucutre

[Navin Shrestha]

I am following this youtube video (https://www.youtube.com/watch?v=tAScTlKW60w) from Jash Banta to install fastSTRCUTURE.  

When doing the ./configure step. The error says : checking for C compiler default output file name... configure: error: C compiler cannot create executables. I then ran the following codes:

     sudo apt-get install build-essential

     sudo apt install libc6-dev

     sudo apt-get install

Despite running these codes, I am still getting the same error (C compiler cannot create executables).

Could anybody share his/her experience to resolve this issue?

Regards,

Navin Shrestha

[Kris van der Gaag]

Hi Navin,

Instead of FastSTRUCTURE you might want to try ezstructure (basically a python3 version of fastSTRUCTURE) which can be installed via the python package index using 'pip install ezstructure'.It's been a while that I used it, but the installation was way more smooth than the earlier version that was not maintained.

Regards,

Kris

[Francisco Pina Martins]

Hello Navin,

fastStructure is *really* hard to install these days, since python2 is mostly gone from every remotely recent GNU/Linux distribution.

ezstructure is a nice alternative, unless you are using the `prior=logistic` option, where it gets kind of slow. If that is not working for you, you can try to generate a faststructure binary using an older Ubuntu image on docker (18.04 will work) - you can follow the instructions here: https://gitlab.com/StuntsPT/Structure_threader/-/blob/master/helper_scripts/install_faststructure.sh?ref_type=heads (or just runt he whole script). I haven't used it in a while, so some things might have changed and need some tweaking.

Alternatively, you can just do `python3 -m pip install structure_threader` which will also install a pre-built faststructure binary for you on `~/.local/bin/faststructure`, or on the appropriate PATH if you are using conda.

Best,

Francisco

[Navin Shrestha]

Hi Kris,

Thank you for your response and for letting me know about ezstructure as an alternative to fastStructure. I tried to work with ezstructure, and while installing pip in ubuntu linux 22.04, I got an error message when I ran $ pip3 --version trying to know the pip3 version installed. The error message is:

Command 'pip3' not found, but can be installed with:
sudo apt install python3-pip

I re-ran the code $ sudo apt install python3-pip, and still got the same error message. I have attached the screenshot below:

I also tried to install the ezstructure in Google Colab, I got following error message:

Error: Could not build wheels for ezstructure, which is required to install pyproject.toml-based projects. Screenshot from Google Colab is attached below:

Would you please not mind in walking me through the steps of ezstructure to install?

Regards,

Navin 

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Sincerely,

Navin Shrestha

Cell no.: +1(919) 670-9005

[Navin Shrestha]

Hi Francisco,

Thank you for making my head clear about the utility of fastStructure in the current scenario where python2 is almost obsolete. I will play with Structure Threader and see if I can grasp the steps and make it worth. I am a very beginner in the field of coding. I will reach out to you if I have any questions.

I really appreciate your concern regarding my queries on fastStrcutre and leading me toward the alternative solution.

Regards,

Navin

[Navin Shrestha]

Hello,

I was able to setup Python2 environment in Ubuntu Linux 20.04 and install fastStructure. I already ran my analysis through STRUCTURE software. And want to run through fastStructure as well. However, I am not being able to convert the files to .bed, .fam and .bim file format. How could I convert them in right format so that I can run it into fastStructure. 

I have attached the input file for STRUCTURE software that I used.

By the way, does fastStructure has the provision of including the name of genotypes on the x-axis?

Regards.

Navin 

[Francisco Pina Martins]

Hi Navin,

You don't have to convert the file to Plink format. You can just modify your STRUCTURE input file to fastStructure. The Structure_threader manual has an entry on how it should look like. Hope this helps.

Best,

Francisco

[Navin Shrestha]

Hi  Francisco,

Thank you for your response. 

I have the output file from GAPIT where the allele dosage is in 0 1 2 format. however looks like fastStructure takes 1 2 3 4 -9 format. Will 0 1 2 be compatible with fastStructure? 

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[Francisco Pina Martins]

Hi again Navin,

As far as I can tell, STRUCTURE also requires the 1 2 3 4 -9 format. I’m not sure how (if) STRUCTURE handles the Homozygous1, Heterozygous, Homozygous2 format. I suppose this is the format you are referring to. Did you run this file through STRUCTURE?

Francisco