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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
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Stoped in the annotation step #119

Closed Wenwen012345 closed 2 years ago

Wenwen012345 commented 2 years ago

Sat Apr 9 02:30:50 CST 2022 Total intact LTR-RTs found: 5470 Total intact non-TGCA LTR-RTs found: 21

Sat Apr 9 02:30:55 CST 2022 Start to annotate whole-genome LTR-RTs... Use -noanno if you don't want whole-genome LTR-RT annotation.

oushujun commented 2 years ago

Hello @wensulin93, can you provide more information? I could not tell anything wrong with the above. - Shujun

Wenwen012345 commented 2 years ago

Sat Apr 9 02:30:55 CST 2022 Start to annotate whole-genome LTR-RTs... Use -noanno if you don't want whole-genome LTR-RT annotation.

just stop in this step: Sat Apr 9 02:30:55 CST 2022 Start to annotate whole-genome LTR-RTs... Use -noanno if you don't want whole-genome LTR-RT annotation.

Ten hours later, no response.

If you choose not to generate the comment file (-noanno), it ends later and only generates.pass.list.gff3; .LTRlib.fa; nmtf.pass.list ; pass.list; LTRlib. Redundant. Fa. And out. The fam. Size. The list; Out. Gff3; Out.superfam.size. List is blank. The species: Rhododendron griersonianum Genome website: https://www.ncbi.nlm.nih.gov/genome/94097

oushujun commented 2 years ago

Hello,

Annotation will take time. Please wait a little longer. There isn't any error information so it may be running correctly. You may also want to fresh restart the analysis if the genome is not too big.

Shujun

Wenwen012345 commented 2 years ago

Okay, that's done. The speed of the previous system was too slow, and the results were achieved quickly by changing the speed of the server.