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Description
I ran into some error when running xpore-dataprep
Command:
xpore-dataprep --eventalign wt1.fastq.evn.aln.tsv --summary wt1.fastq.evn.aln.summary.txt --out_dir wt1_xpore_data_prep
Error:
Process Consumer-1:
Traceback (most recent call last):
File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2646, in get_loc
return self._engine.get_loc(key)
File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'contig'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/users/enovoa/hliu/anaconda3/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
self.run()
File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/xpore/scripts/helper.py", line 77, in run
result = self.task_function(*next_task_args,self.locks)
File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/xpore/scripts/dataprep.py", line 60, in combine
eventalign_result['transcript_id'] = [contig.split('.')[0] for contig in eventalign_result['contig']]
File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/pandas/core/frame.py", line 2800, in getitem
indexer = self.columns.get_loc(key)
File "/nfs/no_backup_isis/enovoa/analysis/hliu/software/XPORE/lib/python3.7/site-packages/pandas/core/indexes/base.py", line 2648, in get_loc
return self._engine.get_loc(self._maybe_cast_indexer(key))
File "pandas/_libs/index.pyx", line 111, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 138, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 1619, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 1627, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'contig'
Input
`==> wt1.fastq.evn.aln.tsv <==
contig position reference_kmer read_index strand event_index event_level_mean event_stdv event_length model_kmer model_mean model_stdv standardized_level start_idx end_idx
chr10 8403 CTATA 1 t 1054 76.79 0.889 0.00232 NNNNN 0.00 0.00 inf 32 39
==> wt1.fastq.evn.aln.summary.txt <==
read_index read_name fast5_path model_name strand num_events num_steps num_skips num_stays total_duration shift scale drift var
1 8c8524ed-fc79-4deb-aafc-d83922ca0b2d wt1/batch_6.fast5 template 1054 171 15 867 6.67 9.819 0.887 0.000 1.797
`
I mapped DRS reads to non-human genome. I wonder if this is what gave me the error?
Thanks for developing this tool and thanks in advance for your help.