Describe the bug
I want to try macsyfinder and TXSScan. I already posted it in the TXSScan repo, where it was identified as a bug.
To Reproduce
I am trying to use macsyfinder with TSScan, however I am running into issues very quickly. I ran the following things after creating a conda environment:
> git clone https://github.com/gem-pasteur/macsyfinder.git
> cd macsyfinder
> python3 -m pip install .
> msf_data install --user TXSScan
Downloading TXSScan (1.1.4).
Extracting TXSScan (1.1.4).
Installing TXSScan (1.1.4) in /nfs/home/lifeer/.macsyfinder/models
Cleaning.
The models TXSScan (1.1.4) have been installed successfully.
> macsyfinder --db-type ordered_replicon --sequence-db Leaf137.fasta -o TXSScan/ --models TXSScan all
MacSyFinder [20260609.dev](http://20260609.dev/)
using:
- Python 3.14.5 | packaged by conda-forge | (main, May 20 2026, 00:15:36) [GCC 14.3.0]
- MacSyLib 1.0.4
- NetworkX 3.6.1
- Pandas 3.0.3
MacSyFinder is distributed under the terms of the GNU General Public License (GPLv3).
See the COPYING file for details.
If you use this software please cite:
Néron, Bertrand; Denise, Rémi; Coluzzi, Charles; Touchon, Marie; Rocha, Eduardo P.C.; Abby, Sophie S.
MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes.
Peer Community Journal, Volume 3 (2023), article no. e28. doi : 10.24072/pcjournal.250.
https://peercommunityjournal.org/articles/10.24072/pcjournal.250/
and don't forget to cite the used models:
msf_data cite <model>
command used: /nfs/lifeer/conda_envs/macsyfinder/bin/macsyfinder --db-type ordered_replicon --sequence-db Leaf137.fasta -o TXSScan/ --models TXSScan all
macsyfinder: "No such model definition: 'TXSScan'"
Expected behavior
I expected macsyfinder to run without an error and use the TXSS model.
Please complete the following information):
OS:
MacSyFinder Version:
MacSyFinder 20260609.dev
using:
- Python 3.14.5 | packaged by conda-forge | (main, May 20 2026, 00:15:36) [GCC 14.3.0]
- MacSyLib 1.0.4
- NetworkX 3.6.1
- Pandas 3.0.3
Describe the bug
I want to try macsyfinder and TXSScan. I already posted it in the TXSScan repo, where it was identified as a bug.
To Reproduce
I am trying to use macsyfinder with TSScan, however I am running into issues very quickly. I ran the following things after creating a conda environment:
Expected behavior
I expected macsyfinder to run without an error and use the TXSS model.
Please complete the following information):
OS:
MacSyFinder Version:
MacSyFinder 20260609.dev
using: