Error with xpore-dataprep

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.

[ploy-np]

Hi @lingolingolin and @mparker2, I’ve mad a new release, xpore-0.5.2 to address these bugs. Hopefully, you can now run xpore on Arabidopsis transcripts using the transcriptome mode in xpore-dataprep. Let me know if you still have problems.

Thank you for your contributions!

[ploy-np]

Hi @lingolingolin ,

I’ve added a feature in xpore-dataprep that users can use their own GTF file to map transcriptome to genome. It’s in ‘gtf’ branch. I’m finding a dataset to test it before I merge with the next release. But it would be very appreciated if you can test this new feature on your own dataset with the genome mode in xpore-dataprep.

Thank you very much in advance!