Open sformel opened 4 years ago
mortonjt
commented
4 years ago Hi @sformel thank you for reporting this error. There has been a dependency issue with pandas v1.0 lately. The easiest fix would be to restrict this version (i.e. conda install pandas==0.25.3).
It'll help to print the contents of env.yaml from conda env export env.yaml to confirm this.
sformel
commented
4 years ago @mortonjt THanks for the quick response! You were correct, downgrading pandas got me past that error, but now I've run up against another:
`Traceback (most recent call last):
File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/matplotlib/font_manager.py", line 1341, in
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/lustre/project/svanbael/steve/conda-envs/songbird_env/bin/songbird", line 3, in
matplotlib=3.2.1=0 matplotlib-base=3.2.1=py37h30547a4_0
mortonjt
commented
4 years ago hmm - that sounds like a matplotlib error. I haven't seen that before - I'd double check your disk space to make sure that you really do have enough space.
The matplotlib folk maybe in a better position to help with this sort of thing. This post should be a good place to get started.
sformel
commented
4 years ago The error messages never lie, do they? There was a huge hidden folder in there causing a ruckus. It's functioning now, thanks for your help!
mortonjt
commented
4 years ago Great!!
On Wed, Apr 8, 2020, 4:00 PM Stephen Formel notifications@github.com wrote:
The error messages never lie, do they? There was a huge hidden folder in there causing a ruckus. It's functioning now, thanks for your help!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/biocore/songbird/issues/128#issuecomment-611216628, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA75VXO4JUTA6E332LMMZ43RLTXWJANCNFSM4MECWTDA .
Samyr-Tachy
commented
4 years ago Instead of using SparseDataFrame() try using pd.DataFrame.sparse.from_spmatrix()
Thanks for developing Songbird, it seems like it will be a useful tool. However, I’m trying to run it as a stand-alone program on our cluster here at Tulane and I’m getting the error below.
When I run the tutorial:
songbird multinomial \ --input-biom songbird-master/data/redsea/redsea.biom \ --metadata-file songbird-master/data/redsea/redsea_metadata.txt \ --formula "Depth+Temperature+Salinity+Oxygen+Fluorescence+Nitrate" \ --epochs 10000 \ --differential-prior 0.5 \ --summary-interval 1 \ --summary-dir resultsI end up with the error
Traceback (most recent call last): File "/lustre/project/svanbael/steve/conda-envs/songbird_env/bin/songbird", line 225, in <module> songbird() File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 829, in __call__ return self.main(*args, **kwargs) File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, **ctx.params) File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 610, in invoke return callback(*args, **kwargs) File "/lustre/project/svanbael/steve/conda-envs/songbird_env/bin/songbird", line 154, in multinomial dense_table = table.to_dataframe().to_dense().T File "/lustre/project/svanbael/steve/conda-envs/songbird_env/lib/python3.7/site-packages/biom/table.py", line 4068, in to_dataframe return constructor(mat, index=index, columns=columns) TypeError: SparseDataFrame() takes no argumentsI apologize if there is an obvious solution, I’m still learning Python. If it’s helpful, this is the output from “conda info”:
active environment : songbird_env active env location : /lustre/project/svanbael/steve/conda-envs/songbird_env shell level : 1 user config file : /home/sformel/.condarc populated config files : /home/sformel/.condarc conda version : 4.5.0 conda-build version : 3.7.2 python version : 3.6.4.final.0 base environment : /share/apps/anaconda/3/5.1.0 (read only) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/noarch https://repo.anaconda.com/pkgs/main/linux-64 https://repo.anaconda.com/pkgs/main/noarch https://repo.anaconda.com/pkgs/free/linux-64 https://repo.anaconda.com/pkgs/free/noarch https://repo.anaconda.com/pkgs/r/linux-64 https://repo.anaconda.com/pkgs/r/noarch https://repo.anaconda.com/pkgs/pro/linux-64 https://repo.anaconda.com/pkgs/pro/noarch package cache : /lustre/project/svanbael/steve/conda_pkgs envs directories : /lustre/project/svanbael/steve/conda-envs /home/sformel/.conda/envs /share/apps/anaconda/3/5.1.0/envs platform : linux-64 user-agent : conda/4.5.0 requests/2.18.4 CPython/3.6.4 Linux/2.6.32-431.23.3.el6.x86_64 centos/6.5 glibc/2.12 UID:GID : 281003972:5043 netrc file : None offline mode : False