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RemiAllio / MitoFinder

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data
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blast problem on ubuntu 22.04 #44

Closed benoitnabholz closed 1 year ago

benoitnabholz commented 1 year ago

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 commented 1 year ago

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 :slightly_smiling_face:

Cheers, Rémi

benoitnabholz commented 1 year ago

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 commented 1 year ago

So the problem seems to be the same as here: https://github.com/RemiAllio/MitoFinder/issues/41 Since singularity is working, it is not urgent at all.

benoitnabholz commented 1 year ago

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 commented 1 year ago

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