mortonjt
commented
4 years ago Hi @bck243 , thanks for reporting.
I'm looking at your biom table, and it looks like there are only 4 samples. Is this correct?
In [1]: import biom
In [2]: from biom import load_table
In [3]: table = load_table('MB_exp1_counts.biom')
In [4]: table
Out[4]: 393094 x 4 <class 'biom.table.Table'> with 1452508 nonzero entries (92% dense)
In [5]: table.ids()
Out[5]: array([' MB1', 'MB2', 'MB3', 'MB4'], dtype=object)If this is the case, then songbird is expected to crash - 10 samples are required at minimum. We'll probably want to include a better error message in the future.
bck243
Hello, I am trying to run songbird on four metatranscriptomic samples from a phytoplankton bloom to see the effect of nitrogen status on gene expression. I've tried to reformat my input data to match the .biom count table and metadata files from the red sea example dataset, but I am getting an error that leads me to believe it is not being read in properly. I have attached my count data as a biom file (converted using
biom convert -i MB_exp1_counts.tsv -o MB_exp1_counts.biom --table-type "OTU table" --to-hdf5) and .tsv, and I've attached my simple metadata .tsv outline which samples are nitrogen replete and deplete.I am running: songbird multinomial \ --input-biom data/MB_exp1_counts.biom \ --metadata-file data/MB_exp1_metadata.tsv \ --formula "nitrogen_condition"
The error is: Traceback (most recent call last): File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/bin/songbird", line 225, in
songbird()
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 829, in call
return self.main(args, kwargs)
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 782, in main
rv = self.invoke(ctx)
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/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 "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
return ctx.invoke(self.callback, ctx.params)
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/lib/python3.7/site-packages/click/core.py", line 610, in invoke
return callback(args, **kwargs)
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/bin/songbird", line 180, in multinomial
seed=random_seed,
File "/usr/local/projdata/0568/projects/PLANKTON/illumina_aallen/bkolody/installations/Miniconda3/envs/songbird_env/lib/python3.7/site-packages/songbird/util.py", line 186, in split_training
i = np.argsort(idx)[num_random_test_examples]
IndexError: index 5 is out of bounds for axis 0 with size 3
I have tried converting the red sea .biom table to .tsv and back, and it the tutorial still works without issue, so I'm not sure what my problem is.
Thanks so much, Bethany Archive.zip