Bug when running end-to-end pipeline report and fix

Hi! I've set genomad v1.9.0 to run on a few _Salmonella_ samples and it seems to run just fine, but throws a tensorflow related error at the end of the geNomad marker-classification step ```` [20:07:51] geNomad marker-classification finished! Traceback (most recent call last): File "/home/malu/anaconda3/envs/genomad2025/bin/genomad", line 10, in <module> sys.exit(cli()) ^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/rich_click/rich_command.py", line 395, in __call__ return super().__call__(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/core.py", line 1462, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/rich_click/rich_command.py", line 209, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/core.py", line 1850, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/core.py", line 1246, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/core.py", line 814, in invoke return callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/decorators.py", line 34, in new_func return f(get_current_context(), *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/genomad/cli.py", line 1368, in end_to_end ctx.invoke( File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/click/core.py", line 814, in invoke return callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/genomad/cli.py", line 772, in nn_classification genomad.nn_classification.main( File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/genomad/modules/nn_classification.py", line 36, in main import tensorflow as tf File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/tensorflow/__init__.py", line 40, in <module> from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow # pylint: disable=unused-import ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/tensorflow/python/pywrap_tensorflow.py", line 34, in <module> self_check.preload_check() File "/home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/tensorflow/python/platform/self_check.py", line 63, in preload_check from tensorflow.python.platform import _pywrap_cpu_feature_guard ImportError: /home/malu/anaconda3/envs/genomad2025/lib/python3.12/site-packages/tensorflow/python/platform/../../libtensorflow_framework.so.2: undefined symbol: _ZN4absl12lts_202501275MutexD1Ev ```` There are files on the output, but not those that should be at the final stage: The genomad output folder has this (as an example of one of the samples): ``` ERX3863107_annotate # folder with some tsvs ERX3863107_annotate.log ERX3863107_find_proviruses # folder with some tsvs ERX3863107_find_proviruses.log ERX3863107_marker_classification # folder with some npz files (besides more tsvs) ERX3863107_marker_classification.log ```` searching on the issues tab I found someone with a similar problem an the sugestion was that it had to do with tensorflow (#65) I had this for the listing of tensorflow (which was impossible to import into python, so there's something wrong there) ``` tensorflow 2.18.1 cpu_py312hbca4264_0 tensorflow-base 2.18.1 cpu_py312h94cdeef_0 ``` I removed that and installed it again with this line: `conda install -y -c conda-forge "tensorflow=2.18.*"` and I apparently broke genomad all together I reinstalled with `conda -install genomad` and it worked! I'm not sure how my report could help or if it's relevant, but it may help someone with a similar problem in the future