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cmayer / MitoGeneExtractor

The MitoGeneExtractor can be used to extract protein coding mitochondrial genes, such as COI and others from short and long read sequencing libraries.
GNU Affero General Public License v3.0
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command not found: MitoGeneExtractor #4

Closed avvypaks closed 1 year ago

avvypaks commented 1 year ago

Hi,

I am not able to run the program after installing it as you have instructed. My exonerate installation was successful. It's still showing:

zsh: command not found: MitoGeneExtractor

Could you please help me with this?

marievalerie commented 1 year ago

Did you try to execute MitoGeneExtractor with the full path?

This is required if you do not add the program to your PATH. If you cloned/downloaded MitoGeneExtractor from the GitHub repository, I would further expect that the executable has a version (1.9.5) number associated with it...

cmayer commented 1 year ago

On Linux/Mac Os you have the PATH variable that contains all directories that the system will look in to find the program. If the binary is not found in any of these directories, you will get this error message. Even if the program binary is in your current working directory, you will need to use "./MiteGeneExtractor" to start the program, unless the directory "." is in the path.

Another potential cause for the error message is: The makefile produces a binary with the name MitoGeneExtractor-v1.9.5 and not just MitoGeneExtractor.

cmayer commented 1 year ago

In the README, I added that the program name is MitoGeneExtractor-vx.y.z where x.y.z is the version number. This should make it more clear. Thanks.

avvypaks commented 1 year ago

It worked after putting it into PATH. Thanks

cmayer commented 1 year ago

The problem is that the exonerate program crashed. Our experience is that a common reason for this problem is that the computer has insufficient RAM to run exonerate. Can you monitor the RAM while MitoGeneExtractor is running and/or try to use computer with more RAM.

We could also try to analyse the data on one of our machines to find the cause of the problem.

avvypaks commented 1 year ago

Thanks for the response. I will try with a server and let you know.

cmayer commented 1 year ago

The issue command not found: MitoGeneExtractor #4 has been resolved.

cmayer commented 1 year ago

Thanks for the response. I will try with a server and let you know.

Can you move this answer to the corresponding issue.

The idea is to have one issue in each issue thread. This thread was created under the title "command not found: MitoGeneExtractor" and people will not look for you problem under this title. So I created a new issue for this problem, to clean up the issues.

cmayer commented 1 year ago

Dear avvypaks,

I would like to move this issue to a new issue. Users who look through the issues will not look for segmentation faults if the heading is "command not found: MitoGeneExtractor".

By the way: Did you run MitoGeneExtractor on a server and did you get results from this?

avvypaks commented 1 year ago

Hi cmayer,

I am getting a different error while running to a linux server. Although the compilation of exonerate was successful, still the program was showing error that it can not make the vulgar file as exonerate is not there. I have tried to put the exonerate prog to my path of MitoGeneExtractor, but still no luck! I am working on a insect genome skim data, Is it possible to try your prog in another way ?

marievalerie commented 1 year ago

Hi, unfortunately, you cannot run MGE without exonerate but I can hardly imagine that exonerate cannot be found if everything is set up properly. Let's see if we can solve the issue :)

Could you please: 1.) post the MitoGeneExtractor command that produced the error and tell me which exonerate version you used. 2.) type ls followed by the /path/to/exonerate that you specified in 1.) and post the output (just to be sure, that there is no spelling mistake)

If it is not related to a simple spelling mistake, please check if the compilation of Exonerate was really successful. You can test that by typing /path/to/exonerate -h and you should see the help page of exonerate and all the options that you can specify.

In principle, if exonerate works, you can run it separately to produce the vulgar file. The vulgar file then, can be used by MGE. Let's see what Christoph suggests in that case.

Alternatively, you can share your data with me privately (m.brasseur@leibniz-lib.de) and I will have a look, if you want.

All the best, Marie

cmayer commented 1 year ago

If you are running MitoGeneExtractor on a HPC cluster with a job system, the path is not automatically exported to the bash environment that runs the job. A simple work arround in this case is to use the -e parameter (in MitoGeneExtractor) to specify the full path to the exonerate program. Marie has also suggested to tun exonerte separately and specify the vulgar file that exonerate produces as an input to the MitoGeneExtractor program.

Best, Christoph