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BioinformaticsToolsmith / Look4LTRs

Long Terminal Repeat Retrotransposon detection tool capable of finding recently nested LTR RTs de novo.
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Problems in testing large genomes #2

Open unavailable-2374 opened 1 year ago

unavailable-2374 commented 1 year ago

Hi Developer

Look4ltrs runs for more than 10h without termination when run on rice(NIP T2T https://www.cell.com/molecular-plant/pdfExtended/S1674-2052(23)00219-8) maize(https://www.nature.com/articles/s41588-023-01419-6#data-availability) human(T2T-CHM13v2.0) log files are active

" Found a nest at level 47 Found a nest at level 47 Found a nest at level 46 "

here is the command : look4ltrs --fasta genome/ --out ./ --parallel 30

Warm regards Shuo

unavailable-2374 commented 1 year ago

I ran it multiple times and found that it would get stuck in one of the same position, even when I ran it on a chromosome alone.

unavailable-2374 commented 1 year ago

hello is anybody there? I masked some part of genome it works, but not on human genome. Look4LTRs still stucks on "Found a nest at level XX", and looks like it can do this endless.

unavailable-2374 commented 10 months ago

Hi Developer

Can this bug be fixed? If it can, I will choose to continue using Look4LTRs in my project, if not, I will have to change my method.

Please contact me if you can.

Best

xiekunwhy commented 7 months ago

@unavailable-2374 , Have you solved this problem? I meet the same situation.

hani-girgis commented 7 months ago

Hi.

We are currently studying this issue and will get back to you as soon as we can.

Best regards.

unavailable-2374 commented 7 months ago

Hi.

We are currently studying this issue and will get back to you as soon as we can.

Best regards. Hi.

Thanks a lot, very much looking forward to your reply.

Best, Cyrus

xiekunwhy commented 7 months ago

Hi.

We are currently studying this issue and will get back to you as soon as we can.

Best regards.

waiting online.

xiekunwhy commented 6 months ago

any progress?

xiekunwhy commented 6 months ago

this problem happen very often, so I think that Look4ltrs is not usable before solving this problem.