Running and Verification

Procedure

Use PuTTY to log in to the server as the root user.
Check whether the installation is successful.
```
cd /path/to/LTR_retriever/LTR_retriever-2.9.0
./LTR_retriever -h
```
Information similar to the following is displayed:

Start the running.

mkdir test && cd test
wget http://ftp.ensembl.org/pub/release-106/fasta/gallus_gallus/dna/Gallus_gallus.GRCg6a.dna.chromosome.16.fa.gz
gunzip Gallus_gallus.GRCg6a.dna.chromosome.16.fa.gz
mv Gallus_gallus.GRCg6a.dna.chromosome.16.fa Gallus.fa
gt suffixerator -db genome.fa -indexname genome.fa -tis -suf -lcp -des -ssp -sds -dna
gt ltrharvest -index genome.fa -minlenltr 100 -maxlenltr 7000 -mintsd 4 -maxtsd 6 -motif TGCA -motifmis 1 -similar 85 -vic 10 -seed 20 -seqids yes > genome.fa.harvest.scn
LTR_retriever -genome genome.fa -inharvest genome.fa.harvest.scn

Information similar to the following is displayed:

Parent topic: LTR_retriever 2.9.0 Porting Guide (Kylin V10)