Skip to content

Error in xpore-dataprep step #24

@madnessfish

Description

@madnessfish

I have encountered some problems while running the xpore-dataprep step. I have mapped the raw DRS reads to human reference transcriptome with minimap2. I wondered if it is related to the read_index in the summary file. Thank you so much!

eventalign.txt
eventalign

summary.txt
summary

command
xpore-dataprep --eventalign eventalign.txt --summary summary.txt --out_dir dataprep

It raise the error below.
Process Consumer-1:
Traceback (most recent call last):
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/xpore/scripts/helper.py", line 77, in run
result = self.task_function(*next_task_args,self.locks)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/xpore/scripts/dataprep.py", line 78, in combine
df2write = df_events_per_read.loc[[tx_id,read_id],:].reset_index()
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 873, in getitem
return self._getitem_tuple(key)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 1044, in _getitem_tuple
return self._getitem_lowerdim(tup)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 766, in _getitem_lowerdim
return self._getitem_nested_tuple(tup)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 847, in _getitem_nested_tuple
obj = getattr(obj, self.name)._getitem_axis(key, axis=axis)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 1099, in _getitem_axis
return self._getitem_iterable(key, axis=axis)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 1037, in _getitem_iterable
keyarr, indexer = self._get_listlike_indexer(key, axis, raise_missing=False)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexing.py", line 1240, in _get_listlike_indexer
indexer, keyarr = ax._convert_listlike_indexer(key)
File "/exeh_2/sin/bin/miniconda3/envs/xpore/lib/python3.8/site-packages/pandas/core/indexes/multi.py", line 2397, in _convert_listlike_indexer
raise KeyError(f"{keyarr[mask]} not in index")
KeyError: "['29dfb566-2dbe-4b8f-8c3e-ba2f6d1403e9'] not in index"

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions