cjw85
commented
1 year ago The medaka CLI contains tools to download models. You can use these to download the models on a node that does have internet access. If you are using a file system shared between you login nodes and HPC nodes then medaka will find the downloaded models automatically.
Hello,
I've been trying to run Medaka consensus from a node in an HPC, however, as the title suggests this node has no access to internet to download the models. Instead I downloaded the model I need ("r104_e81_sup_g610") and placed it in the data folder along with the default models: r104_e81_sup_g610_model.tar.gz in the folder medaka/data. I'm getting the following error after I execute medaka_consensus using a job scheduler:
Traceback (most recent call last):File "/arc/home/jcsm2010/mambaforge/envs/medaka/bin/medaka", line 11, in <module>sys.exit(main())File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/site-packages/medaka/medaka.py", line 724, in main args.func(args)File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/site-packages/medaka/medaka.py", line 267, in is_rle_model print(is_rle_encoder(args.model))File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/site-packages/medaka/medaka.py", line 274, in is_rle_encoder encoder = modelstore.get_meta('feature_encoder')File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/site-packages/medaka/datastore.py", line 193, in get_meta self.unpack()File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/site-packages/medaka/datastore.py", line 118, in unpack with tarfile.open(self.filepath) as tar:File "/arc/home/jcsm2010/mambaforge/envs/medaka/lib/python3.10/tarfile.py", line 1639, in open raise ReadError(f"file could not be opened successfully:\n{error_msgs_summary}")tarfile.ReadError: file could not be opened successfully:- method gz: ReadError('not a gzip file')- method bz2: ReadError('not a bzip2 file')- method xz: ReadError('not an lzma file')- method tar: ReadError('invalid header')Should I specify the full path of the model when I use the -m flag? Or is there anything else I should be doing? I'm using Medaka v 1.8.0 installed via conda(mamba).