mortonjt
commented
3 years ago This error is basically saying that your sample metadata file doesn't have
a Testing column.
You can confirm this if you remove this option.
So likely you either need to add that column, or you don't use it (which it will randomly split your samples into training and testing).
On Fri, Jan 22, 2021 at 12:57 PM bck243 notifications@github.com wrote:
Hello,
I recently closed an issue https://github.com/biocore/songbird/issues/149 about getting the warning warnings.warn('Cannot determine yajl version, assuming <1.0.12') when running the songbird tutorial with qiime version 2020.6. I was able to get the tutorial to work, but the warning always popped up.
Now, running songbird on my own data, I'm still getting the warning and I think it may be the reason songbird won't run.
Here's what I did:
qiime songbird multinomial \ --i-table ./data/P18_16S_all_runs_raw_no_contam_or_control2.qza \ --m-metadata-file ./data/iTAG_metadata_16S_all_for_q2_8_2020.tsv \ --p-formula "CTDPRS" \ --p-epochs 10000 \ --p-differential-prior 0.5 \ --p-training-column Testing \ --p-summary-interval 1 \ --o-differentials CTDPRS_differentials.qza \ --o-regression-stats CTDPRS_regression-stats.qza \ --o-regression-biplot CTDPRS_regression-biplot.qza
Here's the error I get:
/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/ijson/backends/init.py:22: UserWarning: Cannot determine yajl version, assuming <1.0.12 warnings.warn('Cannot determine yajl version, assuming <1.0.12') Plugin error from songbird:
'Testing'
Debug info has been saved to /usr/local/scratch/path/tmp/qiime2-q2cli-err-c8tu95jk.log
And here's the error log:
Traceback (most recent call last): File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Testing'
During handling of the above exception, another exception occurred: (qiime2-2020.6) Fri Jan 22 14:46:48 bkolody@lserver1 /usr/local/path/P18/process_ribotag/songbird/P18_16S
cat /usr/local/scratch/METAGENOMICS/bkolody/tmp/qiime2-q2cli-err-c8tu95jk.log Traceback (most recent call last): File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2897, in get_loc return self._engine.get_loc(key) File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Testing'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/q2cli/commands.py", line 329, in call results = action(arguments) File "
", line 2, in multinomial File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 245, in bound_callable output_types, provenance) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/qiime2/sdk/action.py", line 390, in _callableexecutor output_views = self._callable( view_args) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/q2/_method.py", line 53, in multinomial seed=random_seed, File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/songbird/util.py", line 199, in split_training train_idx = metadata.loc[design.index, training_column] == "Train" File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexing.py", line 1418, in getitem return self._getitem_tuple(key) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexing.py", line 805, in _getitem_tuple return self._getitem_lowerdim(tup) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexing.py", line 929, in _getitem_lowerdim section = self._getitem_axis(key, axis=i) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexing.py", line 1850, in _getitem_axis return self._get_label(key, axis=axis) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexing.py", line 160, in _get_label return self.obj._xs(label, axis=axis) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/generic.py", line 3729, in xs return self[key] File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/frame.py", line 2995, in getitem indexer = self.columns.get_loc(key) File "/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/pandas/core/indexes/base.py", line 2899, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 107, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 131, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1607, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1614, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'Testing'Any help would be appreciated!
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bck243
Hello,
I recently closed an issue about getting the warning
warnings.warn('Cannot determine yajl version, assuming <1.0.12')when running the songbird tutorial with qiime version 2020.6. I was able to get the tutorial to work, but the warning always popped up.Now, running songbird on my own data, I'm still getting the warning and I think it may be the reason songbird won't run.
Here's what I did:
Here's the error I get:
And here's the error log:
Any help would be appreciated!