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m6anet dataprep error #112
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hi Elton, Seems like there is a nan entry in your data somewhere and hence the key error, can you print the first few lines of your eventalign.txt file, the command that you used to run nanopolish eventalign, and maybe provide me with your eventalign.index if it is possible? Thanks! |
Hi Chris, And attached is the gzipped eventalign.index I did a grep -i 'NA' on both files and nothing was retrieved. Hope you can spot the problem. |
hi @eltonjrv, really sorry for my late reply - I have been quite occupied the past few weeks with work. I am not sure yet what's causing this error since the indexing step should be quite straight forward, I think the only way we can troubleshoot this is by printing the transcript_id and read_index that might be causing the error. The error message seems to really indicate that there is a null value in the eventalign.txt. Are you able to install this from github instead and maybe add a try except before line 205 to print the error message just to check?
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Dear developers,
I've already successfully run the full m6anet pipeline (version 2.0.1) on a given dRNA-Seq dataset, but now am experiencing the following error during the dataprep step on a different dRNA-seq dataset.
START of error message
Process Consumer-2:
Traceback (most recent call last):
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/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: nan
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/m6anet/utils/helper.py", line 85, in run
result = self.task_function(*next_task_args,self.locks)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/m6anet/utils/dataprep_utils.py", line 205, in index
pos_end += eventalign_result.loc[_index]['line_length'].sum()
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 1418, in getitem
return self._getitem_tuple(key)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 805, in _getitem_tuple
return self._getitem_lowerdim(tup)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 961, in _getitem_lowerdim
return getattr(section, self.name)[new_key]
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 1418, in getitem
return self._getitem_tuple(key)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 805, in _getitem_tuple
return self._getitem_lowerdim(tup)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 929, in _getitem_lowerdim
section = self._getitem_axis(key, axis=i)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 1850, in _getitem_axis
return self._get_label(key, axis=axis)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/indexing.py", line 160, in _get_label
return self.obj._xs(label, axis=axis)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/generic.py", line 3729, in xs
return self[key]
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/site-packages/pandas/core/frame.py", line 2995, in getitem
indexer = self.columns.get_loc(key)
File "/nobackup/fbsev/bioinformatics-tools/miniconda3/envs/drna-m6anet/lib/python3.7/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: nan
END of error message
It successfully generated the eventalign.index file before printing the the log above.
On the previous steps of the pipeline, nanopolish ran well, like with the first successful dataset, without any apparent error.
I'd appreciate if someone could shed a light.
Many thanks in advance,
Elton
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