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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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No tbl file #134

Closed aijigekoukou-shen closed 1 year ago

aijigekoukou-shen commented 1 year ago

Hello Shujun Ou:

When I run the LTR_retriever, It happened errors as follows:

14:37:21 CST Start to annotate whole-genome LTR-RTs... Use -noanno if you don't want whole-genome LTR-RT annotation.

grep: genome.fa.tbl: No such file or directory famcoverage.pl TE_lib RM_output genome_size_bp > TE_fam.size.list

fam_summary.pl TE_fam.size.list genome_size_bp > TE_fam.sum.txt

perl LTR_sum.pl -genome genome.fa -all genome.fa.RM.out [options] -window [int] bp size of the sliding window, default 3,000,000 -step [int] bp size of the moving step, defalut 300,000 -intact indicate the -all file is an LTR_retriever .pass.list instead of a RepeatMasker .out file sort: cannot read: genome.fa.out: No such file or directory Input file(s) not exist!

The following is my commands:

nohup LTR_retriever -threads 20 -u 7e-9 -genome genome.fa -inharvest genome.fa.LTRharvest.scn -infinder genome.fa.finder.combine.scn > LTR_retriever.log 2>&1 &

Could you give some suggestions?

Thanks

oushujun commented 1 year ago

Hello @aisangekoukou,

Sorry for the delayed response. I can't see any issues here. Have you tried with other genomes or a test data like Arabidopsis?

Thanks, Shujun

aijigekoukou-shen commented 1 year ago

Thanks for your reply. I have already fixed the error with Arabidopsis. I guess it may be because there is only one chromosome in my test data. Thank you for your attention.