EDTA - unknown issue about ltr_finder_parallel HOT 3 CLOSED

Hi Dan,

Thanks for testing EDTA. I am sorry for the inconvenience.

Yes, it's always easier to do things in our own server than to let people use your pipeline - anything can happen in a million ways. We spent a lot of time to make the EDTA pipeline transferrable but there are still a lot of issues. One of the reasons is it tries to combine a number of different pipelines together, which are not necessary bug-free.

From your log file, it seems to be the error of LTR_finder_parallel. Please use your genome to test this pipeline. It's installation free, so just download it and run.

A good practice I should have put in the instruction - always prepare your genome file with simple sequence names - no special characters, just letters and numbers and try to keep them short (i.e., <25 characters).

Please let me know if you encounter any errors.

Best,
Shujun

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Hi Shujun,

thanks for the suggestion. I tried LTR_FINDER_parallel on a sequence with name >000000F-023-01|quiver_obj ALT_Parent:Super-Scaffold_1125 and it failed with similar issues to that in the log file I attached above. Changing the name to scaff1 solved the issue. So I think you are right that it was just a scaffold naming issue. If not already, it would be useful if you could mention this in the help / tutorial.

Thanks for your help

Best

Dan

from ltr_finder_parallel.

Hi Shujun,

Just to let you know that changing the scaffold names worked so the issue can be closed

Thanks for your help

Dan

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