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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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Problem running the program #37

Closed luishdez35 closed 2 years ago

luishdez35 commented 2 years ago

Hello, I try to run again MItofinder, but I have the next problem:

Traceback (most recent call last): File "/opt/anaconda3/envs/mitofinder2/bin/MitoFinder/mitofinder", line 1209, in <module> rename = Popen(args1, stdout=open(os.devnull, 'wb')) File "/opt/anaconda3/envs/mitofinder2/lib/python2.7/subprocess.py", line 394, in __init__ errread, errwrite) File "/opt/anaconda3/envs/mitofinder2/lib/python2.7/subprocess.py", line 1047, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

The program seems to found contigs but doesn't finish

I hope you can help me with this, I ran Mitofinder last year without problems

Best

RemiAllio commented 2 years ago

Hello,

I don't know if it comes from that but it seems you are using an Anaconda3 environment. However, MitoFinder is still written in Python2 (unfortunately) so could you please confirm that you are using python2.7 to run it?

Have you tried using the singularity container to avoid any "installation" issues?

Sorry for the inconvenience... Cheers, Rémi

luishdez35 commented 2 years ago

Hello Remi, Yes, I am using python 2.7 in my conda environment; I will try the singularity container, I don how to use it, but I figure it out.

Best

RemiAllio commented 2 years ago

Please see Run MitoFinder with Singularity and let me know if I can help you!

luishdez35 commented 2 years ago

Perfecto, I will do that.

Thanks

RemiAllio commented 2 years ago

Sorry again for the inconvenience ...

luishdez35 commented 2 years ago

Work perfect running with Singularity, thanks.

Best

RemiAllio commented 2 years ago

Nice! Thanks for your feedback 🙂