blast problem on ubuntu 22.04

[benoitnabholz]

Hi Remi,

I have a problem with the makeblastdb available with MitoFinder on ubuntu 22.04:
MitoFinder/blast/bin/makeblastdb: error while loading shared libraries: libidn.so.11: cannot open shared object file: No such file or directory

I tried made a symbolic link my version of blast but the pipeline doesn't work and I fear it could be because of that (not sure).

Cheers,
Benoit

[RemiAllio]

Hi Benoit,

Could you please try to specify the path of your blast executables in the MitoFinder config file (Mitofinder.config) instead of creating a symbolic link?
Do you confirm that your executable works outside MitoFinder? I guess so, but just to be sure...
If not, you will need to install the libidn.so.11 library (you can try sudo yum install libidn.x86_64).

Finally, you still can try the singularity container of MitoFinder 🙂

Cheers,
Rémi

[benoitnabholz]

Hi Rémy,

Singularity is working very well. I just wanted to let you know some issue with ubuntu 22.04.
So the problem doesn't come makeblastdb as putting the path in Mitofinder.config solves the problem.
I still have this error:

Creating summary statistics for mtDNA contig 1

Traceback (most recent call last):
File "/home/benoitnabholz/softwares/MitoFinder/mitofinder", line 1209, in
rename = Popen(args1, stdout=open(os.devnull, 'wb'))
File "/usr/lib/python2.7/subprocess.py", line 394, in init
errread, errwrite)
File "/usr/lib/python2.7/subprocess.py", line 1047, in _execute_child
raise child_exception
OSError: [Errno 2] No such file or directory

And nothing is in the folder *_MitoFinder_arwen_Final_Results except the *.infos file.

Benoit

[benoitnabholz]

So the problem seems to be the same as here: #41
Since singularity is working, it is not urgent at all.

[benoitnabholz]

I understood. The problem came from the path of the python2 interpreter.

If I change all the "/usr/bin/python" by "/usr/bin/python2" in the *.py files of MitoFinder, then MitoFinder is working as expected.

[RemiAllio]

Nice, well spotted!
I need to translate the scripts in python 3. One day...
Cheers!
Rémi

[Isoris]

conda / mamba create -n mitofinder_env python=2.7

cd MitoFinder

which python2.7

then use sed

sed -i 's|#!/usr/bin/python2|#!ADDTHEPATHHERE|' mitofinder