oushujun
commented
7 months ago Hello,
Please update to the latest GitHub version and run again. The current conda version has an identified bug reported in Issue.
Shujun
On Sun, Nov 26, 2023 at 11:10 PM 44314474 @.***> wrote:
Hello! When i used LTR_retriever, the output files:fa.mod.nmtf.pass.list and fa.mod.defalse are empty.
The code is :LTR_retriever -genome ./Gallus_gallus.fa -inharvest /public/home/wml/Repeat/02.insert_time/Gallus_gallus/02.LTR_harvest/Gallus_gallus.fa.harvest.combine.scn -infinder /public/home/wml/Repeat/02.insert_time/Gallus_gallus/01.LTR_finder/Gallus_gallus.fa.finder.combine.scn -threads 40
These are the messages that generated :Sun Nov 26 16:50:12 CST 2023 Dependency checking: All passed! Sun Nov 26 16:50:16 CST 2023 LTR_retriever is starting from the Init step. Sun Nov 26 16:50:28 CST 2023 The longest sequence ID in the genome contains 19 characters, which is longer than the limit (13) Trying to reformat seq IDs... Attempt 1... Attempt 2... Sun Nov 26 16:50:40 CST 2023 Seq ID conversion successful!
Sun Nov 26 16:50:50 CST 2023 Start to convert inputs... Total candidates: 3240 Total uniq candidates: 3240
Sun Nov 26 16:51:04 CST 2023 Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded.
Sun Nov 26 16:51:04 CST 2023 3165 clean candidates remained
Sun Nov 26 16:51:04 CST 2023 Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step.
Invalid value for shared scalar at /public/home/wml/miniconda3/envs/genome_annotation/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 331. Sun Nov 26 16:52:35 CST 2023 Intact LTR-RT found: 0
cp: cannot stat ‘Gallus_gallus.fa.mod.retriever.scn.adj’: No such file or directory Sun Nov 26 16:52:35 CST 2023 No LTR-RT was found in your data.
Sun Nov 26 16:52:35 CST 2023 All analyses were finished!
But i have no idea to deal with this :Invalid value for shared scalar at /public/home/wml/miniconda3/envs/genome_annotation/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 331.
Any help or suggestions would be greatly appreciated. Thanks!
— Reply to this email directly, view it on GitHub https://github.com/oushujun/LTR_retriever/issues/159, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NGL4LEVRSOHD5X6ZJ3YGQHDNAVCNFSM6AAAAAA73MYJQGVHI2DSMVQWIX3LMV43ASLTON2WKOZSGAYTCNBUGY4TINA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Hello! When i used LTR_retriever, the output files:fa.mod.nmtf.pass.list and fa.mod.defalse are empty.
The code is :LTR_retriever -genome ./Gallus_gallus.fa -inharvest /public/home/wml/Repeat/02.insert_time/Gallus_gallus/02.LTR_harvest/Gallus_gallus.fa.harvest.combine.scn -infinder /public/home/wml/Repeat/02.insert_time/Gallus_gallus/01.LTR_finder/Gallus_gallus.fa.finder.combine.scn -threads 40
These are the messages that generated :Sun Nov 26 16:50:12 CST 2023 Dependency checking: All passed! Sun Nov 26 16:50:16 CST 2023 LTR_retriever is starting from the Init step. Sun Nov 26 16:50:28 CST 2023 The longest sequence ID in the genome contains 19 characters, which is longer than the limit (13) Trying to reformat seq IDs... Attempt 1... Attempt 2... Sun Nov 26 16:50:40 CST 2023 Seq ID conversion successful!
Sun Nov 26 16:50:50 CST 2023 Start to convert inputs... Total candidates: 3240 Total uniq candidates: 3240
Sun Nov 26 16:51:04 CST 2023 Module 1: Start to clean up candidates... Sequences with 10 missing bp or 0.8 missing data rate will be discarded. Sequences containing tandem repeats will be discarded.
Sun Nov 26 16:51:04 CST 2023 3165 clean candidates remained
Sun Nov 26 16:51:04 CST 2023 Modules 2-5: Start to analyze the structure of candidates... The terminal motif, TSD, boundary, orientation, age, and superfamily will be identified in this step.
Invalid value for shared scalar at /public/home/wml/miniconda3/envs/genome_annotation/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 331.
Sun Nov 26 16:52:35 CST 2023 Intact LTR-RT found: 0
cp: cannot stat ‘Gallus_gallus.fa.mod.retriever.scn.adj’: No such file or directory Sun Nov 26 16:52:35 CST 2023 No LTR-RT was found in your data.
Sun Nov 26 16:52:35 CST 2023 All analyses were finished!
But i have no idea to deal with this :Invalid value for shared scalar at /public/home/wml/miniconda3/envs/genome_annotation/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 331.
Any help or suggestions would be greatly appreciated. Thanks!