sestaton/tephra

run failed

ShowkyBioinformatics opened this issue · 2 comments

ShowkyBioinformatics commented

When i run the tephra to indentify the TE on a new genome, and i had faild with the following problems:
Use of uninitialized value $chromosome in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.
Use of uninitialized value $start in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.
Use of uninitialized value $end in concatenation (.) or string at lib/site_perl/5.14.0/Tephra/Role/Util.pm line 41.

[ERROR]: Something went wrong fetching sequence for ':-'. Got zero length.
at lib/site_perl/5.14.0/Tephra/Genome/Unmask.pm line 78.

sestaton commented

I would need to see your configuration file and/or the command you used to diagnose this message.

Though, I suspect you have weird symbols in your sequence name such as ":" and "-" or similar. Can you confirm this or comment further?

Thanks.

sestaton commented

Hi again,

Could you please provide an update? Without some understanding of the input or the command that was given there is no way to debug the error.

Also, I made a new major release yesterday with lots of changes. If you can, give that new version (v0.12.0) a try and see if that solves the problem.

Thanks.