Spontaneous error with python "index out of range" about getorganelle HOT 3 CLOSED

This issue happened after v1.6.0 when "blastn" is not executable. You can prove this by executing /home/svillanu/Programs/GetOrganelle/GetOrganelleDep/linux/ncbi-blast/blastn -version directly, you would probably get "/lib64/libc.so.6: version `GLIBC_2.14' not found". This happened because the attached ncbi-blast version may be too high for your system. I guess you got this issue because you updated GetOrganelle after you finished the previous successful chloroplast running.

One temporary solution for this is ①if you installed GetOrganelle in the in situ way, delete the folder /home/svillanu/Programs/GetOrganelle/GetOrganelleDep/linux/ncbi-blast/ (GetOrganelle would then automatically use the blastn in the $PATH); ②if you installed GetOrganelle in the setup.py way, delete the folder /home/svillanu/Programs/GetOrganelle/GetOrganelleDep/linux/ncbi-blast/ then use the pip to reinstall. I guess you used the in situ way.

I would fix or at least give better instruction for this issue in the coming v1.6.2 (under testing and almost done). Good luck with your study!

from getorganelle.

You were absolutely right, GLIBC_2.14 was the problem. I have been familiar with this kind of issues with other programs.

I deleted the folder as you said, and installed blast from bioconda in the same environment where I put the python packages. Seems like it solved the problem as both are running right now.

Just as a curiosity, have you considered making a bioconda package for GetOrganelle? Would make it way easier to install and I think would help to alleviate this kind of dependencies issues.

Thanks for the fast reply and the solution!

from getorganelle.

Thanks for the suggestion. I would add it to the plan, although it would not be very soon.

from getorganelle.