smirarab
AttributeError: 'Namespace' object has no attribute 'pasta'
Hi, I`ve installed sepp and pasta from bioconda and have been trying to execute run_upp.py under conda environment, but I get the following error:
[10:38:24] config.py (line 349): INFO: Seed number: 297834
[10:38:24] exhaustive_upp.py (line 63): INFO: Reading input sequences: <_io.TextIOWrapper name='NZZ_SPL_prot.faa' mode='r' encoding='UTF-8'>
[10:38:24] exhaustive_upp.py (line 96): INFO: Backbone size set to: 39
[10:38:24] exhaustive_upp.py (line 105): INFO: Writing backbone set.
[10:38:24] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/NZZ_brara._ujhe5wf
[10:38:24] exhaustive_upp.py (line 109): INFO: Generating pasta backbone alignment and tree.
Traceback (most recent call last):
File "/home/d.omelchenko/miniconda3/envs/dom/bin/run_upp.py", line 25, in
Can you report the sepp version you are using?
run_sepp.py -v
On Sat, Nov 14, 2020 at 11:50 PM Omdeno [email protected] wrote:
Hi, I`ve installed sepp and pasta from bioconda and was trying to execute run_upp.py under conda environment, but I get the following error:
[10:38:24] config.py (line 349): INFO: Seed number: 297834 [10:38:24] exhaustive_upp.py (line 63): INFO: Reading input sequences: <_io.TextIOWrapper name='NZZ_SPL_prot.faa' mode='r' encoding='UTF-8'> [10:38:24] exhaustive_upp.py (line 96): INFO: Backbone size set to: 39 [10:38:24] exhaustive_upp.py (line 105): INFO: Writing backbone set. [10:38:24] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/NZZ_brara._ujhe5wf [10:38:24] exhaustive_upp.py (line 109): INFO: Generating pasta backbone alignment and tree. Traceback (most recent call last): File "/home/d.omelchenko/miniconda3/envs/dom/bin/run_upp.py", line 25, in main() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 450, in main UPPExhaustiveAlgorithm().run() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/algorithm.py", line 153, in run self.check_options() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 162, in check_options self.generate_backbone() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 110, in generate_backbone pastaalignJob = PastaAlignJob() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/jobs.py", line 733, in init ExternalSeppJob.init(self, self.job_type, **kwargs) File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/jobs.py", line 59, in init self.job_type).path AttributeError: 'Namespace' object has no attribute 'pasta'
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-- Siavash Mirarab
Also, I have a hypothesis about what is going on. Have you run the third step in the installation steps?
https://github.com/smirarab/sepp/blob/master/README.UPP.md#installation-steps
My guess is that you have not run python setup.py upp or python setup.py upp -c.
On Wed, Nov 18, 2020 at 11:42 AM siavash mirarab [email protected] wrote:
Can you report the sepp version you are using?
run_sepp.py -v
On Sat, Nov 14, 2020 at 11:50 PM Omdeno [email protected] wrote:
Hi, I`ve installed sepp and pasta from bioconda and was trying to execute run_upp.py under conda environment, but I get the following error:
[10:38:24] config.py (line 349): INFO: Seed number: 297834 [10:38:24] exhaustive_upp.py (line 63): INFO: Reading input sequences: <_io.TextIOWrapper name='NZZ_SPL_prot.faa' mode='r' encoding='UTF-8'> [10:38:24] exhaustive_upp.py (line 96): INFO: Backbone size set to: 39 [10:38:24] exhaustive_upp.py (line 105): INFO: Writing backbone set. [10:38:24] filemgr.py (line 129): INFO: Root temp directory built: /tmp/sepp/NZZ_brara._ujhe5wf [10:38:24] exhaustive_upp.py (line 109): INFO: Generating pasta backbone alignment and tree. Traceback (most recent call last): File "/home/d.omelchenko/miniconda3/envs/dom/bin/run_upp.py", line 25, in main() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 450, in main UPPExhaustiveAlgorithm().run() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/algorithm.py", line 153, in run self.check_options() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 162, in check_options self.generate_backbone() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/exhaustive_upp.py", line 110, in generate_backbone pastaalignJob = PastaAlignJob() File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/jobs.py", line 733, in init ExternalSeppJob.init(self, self.job_type, **kwargs) File "/home/d.omelchenko/miniconda3/envs/dom/lib/python3.7/site-packages/sepp/jobs.py", line 59, in init self.job_type).path AttributeError: 'Namespace' object has no attribute 'pasta'
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-- Siavash Mirarab
-- Siavash Mirarab
No, I didn't used setup.py script. It is sepp v. 4.3.10, I've installed it from bioconda channel (conda install -c bioconda sepp). Should there be setup.py file somewhere in conda package installation folder? I thought conda packages install without additional setup scripts. I think I found the problem. It seems that file upp.config is missing in folder miniconda3/envs/dom/share/sepp/sepp. There is only main.config. If I copy main.config and rename it to upp.config, and append pasta path in it: [pasta] path=/path/to/run_pasta.py UPP runs, but throws another error that it can't find mafft, as it is looking in the wrong bin folder. I've added "export PASTA_TOOLS_DEVDIR=$CONDA_PREFIX/bin/" to .bashrc, and now run_upp.py works without errors.
Thanks. I will keep this issue open to figure out a way to fix the bioconda installation to work with UPP as well. Right now, the bioconda installation only works for SEPP.
On Wed, Nov 18, 2020 at 12:14 PM Omdeno [email protected] wrote:
No, I havent used setup.py script. It is sepp v. 4.3.10, Ive installed it from bioconda channel (conda install -c bioconda sepp). Should there be setup.py file somewhere in conda package installation folder? I thought conda packages install without additional setup scripts. I think I found the problem. It seems that file upp.config is missing in folder miniconda3/envs/dom/share/sepp/sepp. There is only main.config. If I copy main.config and rename it to upp.config, and append pasta path in it: [pasta] path=/path/to/run_pasta.py UPP runs, but throws another error that it cant find mafft, as it is looking in the wrong bin folder. Ive added "export PASTA_TOOLS_DEVDIR=$CONDA_PREFIX/bin/" to .bashrc, and now run_upp.py works without errors.
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-- Siavash Mirarab