oushujun
commented
4 years ago Hello,
If you have not, please update LTR_retriever to v2.7 and try again.
Please use the Arabidopsis genome to test on the pipeline and make sure it's correctly installed.
If you are testing the pipeline with a small subset of your data, try to run it on the full set. It's pretty quick. The wheat genome took 8 days.
If it works properly, and still says limited intact LTR and total LTR, that's what it literally means. Not all species has abundant and avtive LTR retrotransposons.
Hope these helps!
Best, Shujun
On Fri, Oct 25, 2019, 2:38 AM 123guoxiaoyu notifications@github.com wrote:
Hello, I am running LTR retriever, and I am coming across these errors: 1.when i run /LTR_retriever/LTR_retriever,It displays the following error, but it can continue to run. Fri Oct 25 06:19:16 Local time zone must be set--see zic manual page 2019 1 truncated LTR-RTs found Warning: LOC list /dellfsqd2/ST_OCEAN/USER/zhangrui/test/guo/Flow_test/rawdata/smdlt_test.part-1.fa.ltrTE.veryfalse is empty. 2.finally,it displays the following error,I want to know whether the reason for this error is that there are too few LTRs in my input file, or there is a problem with my operation. Fri Oct 25 06:31:10 Local time zone must be set--see zic manual page 2019 The identity of LTR sequences: 88.7317261904762%
【Warning】 The identity drops below the safe limit. Instead, identity of 92% will be used for LAI adjustment.Fri Oct 25 06:31:10 Local time zone must be set--see zic manual page 2019 Calculate LAI:
【Error】Intact LTR-RT content (0.02%) is too low for accurate LAI calculation (min 0.1% required) 【Error】 Total LTR sequence content (0.3%) is too low for accurate LAI calculation (min 5% required) Sorry, LAI is not applicable on the current genome assembly.Fri Oct 25 06:31:13 Local time zone must be set--see zic manual page 2019 All analyses were finished! 3.(1)Here are example commands that lead to the error： ./ltr_finder -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.8 ./rawdata/smdlt_test.fa > ./rawdata/smdlt.finder.scn (2)./LTR_retriever -threads 4 -genome ./rawdata/1.fa -infinder ./rawdata/1.finder.scn my input file is a whole genome.fa Any ideas as to what the issue is? Thank you!
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123guoxiaoyu
Hello, I am running LTR retriever, and I am coming across these errors: 1.when i run /LTR_retriever/LTR_retriever,It displays the following error, but it can continue to run. Fri Oct 25 06:19:16 Local time zone must be set--see zic manual page 2019 1 truncated LTR-RTs found Warning: LOC list /dellfsqd2/ST_OCEAN/USER/zhangrui/test/guo/Flow_test/rawdata/smdlt_test.part-1.fa.ltrTE.veryfalse is empty. 2.finally,it displays the following error,I want to know whether the reason for this error is that there are too few LTRs in my input file, or there is a problem with my operation. Fri Oct 25 06:31:10 Local time zone must be set--see zic manual page 2019 The identity of LTR sequences: 88.7317261904762%
Fri Oct 25 06:31:10 Local time zone must be set--see zic manual page 2019 Calculate LAI:
Fri Oct 25 06:31:13 Local time zone must be set--see zic manual page 2019 All analyses were finished! 3.(1)Here are example commands that lead to the error： ./ltr_finder -D 15000 -d 1000 -L 7000 -l 100 -p 20 -C -M 0.8 ./rawdata/smdlt_test.fa > ./rawdata/smdlt.finder.scn (2)./LTR_retriever -threads 4 -genome ./rawdata/1.fa -infinder ./rawdata/1.finder.scn my input file is a whole genome.fa Any ideas as to what the issue is? Thank you!