'ValueError' object has no attribute 'message'

[Cai-98]

When running the software in docker, the following error was encountered : 'ValueError' object has no attribute 'message' in Counting feature regions, Counting annotated intermediate exons and Estimating gene expression. By browsing the code, there may be a problem with AnalysisUnit.count.

[fgypas]

Hi @Cai-98

Thank you for reporting this.
Can you please provide me with the alignment file (or part of it) that you are using in order to try to debug it?

Thank you in advance

[Cai-98]

Hi @Cai-98

Thank you for reporting this.
Can you please provide me with the alignment file (or part of it) that you are using in order to try to debug it?

Thank you in advance

Thank you for your reply. Part of file can be download here. And human GRCh38.87 support level 5 annotation files are used while running.

[haiyonghe]

Hi fgypas！
I also encountered this problem. What method should I use to solve this bug?

Thank you in advance

[Cai-98]

Hi fgypas！
I also encountered this problem. What method should I use to solve this bug?

Thank you in advance

The encoding of chromosome in your file and reference file. (like "chr3" and "3"), and not sorting by coordinate are two causes I've found.

[haiyonghe]

Thank you so much for your reply.
In order to ensure that the bam file can run, can you please tell me the download address of the bam file used by TECtool.

Thank you

[fgypas]

Hi,
Sorry, I did not have time to work on the issue yet, but if it is like @Cai-98 describes then it should be easy to add a check in the very beginning.

@haiyonghe I would recommend to make a test run with the files we provide here: https://github.com/zavolanlab/TECtool#recommended-files-for-testing

Let me know if that works.