AssertionError

[Geil625]

Hi,

First thanks for the nice tool to study TE by long reads. The Preprocessing step ran smoothly in my dataset. But when I applied LocusMasterTE bulk assign, I got an error like:

I wonder if you have any ideas regarding this issue.

By the way, the demo sample_alignment_sort.bam under LocusMasterTE/data seems not be sorted by name, which violates the requirement mentioned in the main page. Is that right?

Thanks in advance.
Sang

[LEESojung1998]

Hi,

First, thank you for pointing out the issue with the demo file. I have uploaded a new demo file that has been sorted by name. Thank you again.

Regarding the assertion error, I believe it has occurred due to the GTF file. As you may already know, LocusMasterTE is built upon Telescope, and it uses functions from Telescope. The merge_intervals function at _annotation_intervaltree.py can only merge two overlapped regions. So, when the number of regions increases to three or more, the script may raise an assertion error.

I will define a new function that can merge several overlapped regions in the next round of updates for LocusMasterTE. But for now, to resolve this issue, you can try merging or removing those contigs before running LocusMasterTE.

Best,
Sojung