search

oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
176 stars 40 forks source link

LAI seems not working... #116

Closed xiahouzuoying closed 2 years ago

xiahouzuoying commented 2 years ago

Hi The software has already generated the files shown in the screenshot, however, the Harvest file has not changed for a week. I don't know whether there is a problem, the system still shows running.

Your best Zuoying image

oushujun commented 2 years ago

Hello Zuoying,

This is not yet the LAI step. If your LTRharvest is stuck, you may re-run it. You may also consider this multi-threading version: https://github.com/oushujun/LTR_HARVEST_parallel

Best, Shujun

xiahouzuoying commented 2 years ago

Hi Dr. Ou

Thank you for your answer. I will try to re-run it.

Best, Zuoying

oushujun commented 2 years ago

Any lucks?

xiahouzuoying commented 2 years ago

Hi Dr. Ou

I've tried to use the parallel version, the error file has many errors like below: image and the scn file showed this: image I don't know why...

Best, Zuoying

oushujun commented 2 years ago

Please use default parameters.

Shujun

On Sun, Apr 24, 2022 at 11:04 PM Zuoying Xiahou @.***> wrote:

Hi Dr. Ou

I've tried to use the parallel version, the error file has many errors like below: [image: image] https://user-images.githubusercontent.com/57342415/165013834-283e3ca9-5f79-4b05-af5a-880e2c29c1a0.png and the scn file showed this: [image: image] https://user-images.githubusercontent.com/57342415/165013908-d5ff49b3-f163-4464-84ff-7547c49c896c.png I don't know why...

Best, Zuoying

— Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/116#issuecomment-1108017744, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDR5WFRW7PLVFW4GYLVGYDT5ANCNFSM5QFM5GAA . You are receiving this because you commented.Message ID: @.***>

xiahouzuoying commented 2 years ago

Dear Dr. Ou I finally found the point. Because the contigs ID (Canu results) has too much information, the parallel version works fine after simplify the ID.

Best wishes Zuoying

Please use default parameters. Shujun … On Sun, Apr 24, 2022 at 11:04 PM Zuoying Xiahou @.> wrote: Hi Dr. Ou I've tried to use the parallel version, the error file has many errors like below: [image: image] https://user-images.githubusercontent.com/57342415/165013834-283e3ca9-5f79-4b05-af5a-880e2c29c1a0.png and the scn file showed this: [image: image] https://user-images.githubusercontent.com/57342415/165013908-d5ff49b3-f163-4464-84ff-7547c49c896c.png I don't know why... Best, Zuoying — Reply to this email directly, view it on GitHub <#116 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDR5WFRW7PLVFW4GYLVGYDT5ANCNFSM5QFM5GAA . You are receiving this because you commented.Message ID: @.>

oushujun commented 2 years ago

@xhzy940301 Glad that you found the issue. It's always recommended (or required) to simplify your sequence IDs before any analysis. Good luck with your project! - Shujun