warning message: "Problem encountered while correcting transcript " single positional indexer is out-of-bounds

[criphg]

I have facing the follow error:

/home/yanlab/Tools/TranscriptClean/TranscriptClean.py:449: UserWarning: Problem encountered while correcting transcript with ID 51ae56aa-43a8-4e20-bbc5-85ed8ea749bb. Will output original version. warnings.warn(("Problem encountered while correcting transcript " single positional indexer is out-of-bounds /home/yanlab/Tools/TranscriptClean/TranscriptClean.py:449: UserWarning: Problem encountered while correcting transcript with ID ef176324-7623-4a17-8caf-a50ae7ed7859. Will output original version. warnings.warn(("Problem encountered while correcting transcript " single positional indexer is out-of-bounds /home/yanlab/Tools/TranscriptClean/TranscriptClean.py:449: UserWarning: Problem encountered while correcting transcript with ID dfa9ff9b-1b1c-48ce-9ae8-b803c3ffbb6a. Will output original version. warnings.warn(("Problem encountered while correcting transcript " single positional indexer is out-of-bounds /home/yanlab/Tools/TranscriptClean/TranscriptClean.py:449: UserWarning: Problem encountered while correcting transcript with ID 8f1a89de-355a-431a-b6d3-721a49d84f85. Will output original version. warnings.warn(("Problem encountered while correcting transcript " single positional indexer is out-of-bounds

The command lines used:

python ./accessory_scripts/get_SJs_from_gtf.py --f GRCh38_basic.gtf --g GRCh38.fa --o sj_file.tsv python ./TranscriptClean.py -t 20 -s sample.sam -g GRCh38.fa -o output_file -j sj_file.tsv

Could you help me?

[criphg]

I forgot to mention the GRCh38_basic.gtf and GRCh38.fa was downloaded from gencode. Gtf. Minimap2 was used to alignment: minimap2 -ax splice --MD -k14 -uf --secondary=no -t 20 path_ont_fastq

[callumparr]

I also get many of these errors but until have been ignoring them.

[saberiato]

Same here... received huge number of the same Exception... @fairliereese do you have any idea why is this Exception raised (TranscriptClean.py : Line 447)?