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GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing
https://xpore.readthedocs.io/
MIT License
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xpore-diffmode error #54

Closed al3xMlt closed 2 years ago

al3xMlt commented 3 years ago

Hello During processing xpore-diffmode showed following error:

Using the signal of unmodified RNA from /home/amalt/miniconda3/envs/py39/lib/python3.9/site-packages/xpore/diffmod/model_kmer.csv 19620 ids to be testing ... Traceback (most recent call last): File "/home/amalt/miniconda3/envs/py39/bin/xpore-diffmod", line 8, in sys.exit(main()) File "/home/amalt/miniconda3/envs/py39/lib/python3.9/site-packages/xpore/scripts/diffmod.py", line 190, in main data_dict[(condition_name,run_name)] = ujson.loads(json_str) # A data dict for each gene. ValueError: Trailing data

However, xpore has already processed 100 transcripts and then suddenly breaks off in the middle after the 100th transcript.

Thanks in advance!

ploy-np commented 3 years ago

Hi @al3xMlt,

Can I ask if the last line of data.log shows "--- SUCCESSFULLY FINISHED ---"?

al3xMlt commented 3 years ago

both dataprep files are "--- SUCCESSFULLY FINISHED ---" but the diffmode data.log doesn't. It ends with the transcript where the error occurred

ploy-np commented 3 years ago

Hi @al3xMlt,

Sorry for the slow response! Do you still have this problem? It seems that data.json for that specific transcript is malformed. Could you look in the data.json file at the specific transcript? Or is it possible to share the data.json file by email so that I can explore more about this error?