Open IdoBar opened 12 months ago
Hi Ido, I suspect the versions of Bifrost used to build the graph and in unitig-caller may be different, meaning unitig-caller cannot read the Bifrost input files. Would you be able to check this, please?
Hi @samhorsfield96 and thanks for the quick reply.
I've used Bifrost
is v1.2.0 to generate the graphs, do you recommend trying with unitig-caller
v1.2.0 or updating Bifrost
to the recent version (v1.2.1)? Is the latest Bifrost
compatible with unitig-caller
v1.3.0
Thanks, Ido
I tried running with unitig-caller
v1.2.0 (installed at a separate conda
env and I'm getting the following error:
Traceback (most recent call last):
File "/home/ibar/miniconda3/envs/gwas2/bin/unitig-caller", line 7, in <module>
srun: error: bun111: task 0: Exited with exit code 1
from unitig_caller.__main__ import main
File "/home/ibar/miniconda3/envs/gwas2/lib/python3.9/site-packages/unitig_caller/__main__.py", line 11, in <module>
import unitig_query
ImportError: /home/ibar/miniconda3/envs/gwas2/lib/python3.9/site-packages/unitig_query.cpython-39-x86_64-linux-gnu.so: undefined symbol: _ZN12KmerIteratordeEv
Any idea what's happening?
Hi Ido, the version of Bifrost used to build the graph (v1.2.0) needs to match that used in the unitig-caller environment. I don't believe the version of unitig-caller should matter in this case, as the functions from Bifrost that are used are the same, it is just the graph data structure that is different. I would suggest reinstalling unitig-caller and specifying the Bifrost version you require.
For example:
conda install unitig-caller bifrost=1.2.0
Hi,
I'm trying to run
unitig-caller
(v1.3.0 installed usingbioconda
) on an HPC using a population graph that I generated withbifrost
. The command I'm using is:And I'm getting the following output:
This are the details of the operating system on the HPC:
Thanks, Ido