使用conda安装好EDTA环境

$ EDTA.pl

#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0  #####
##### Shujun Ou (shujun.ou.1@gmail.com)             #####
#########################################################


Parameters:


At least 1 parameter is required:
1) Input fasta file: --genome

This is the Extensive de-novo TE Annotator that generates a high-quality
structure-based TE library. Usage:

perl EDTA.pl [options]
        --genome [File]         The genome FASTA file. Required.
        --species [Rice|Maize|others]   Specify the species for identification of TIR
                                        candidates. Default: others
        --step [all|filter|final|anno]  Specify which steps you want to run EDTA.
                                        all: run the entire pipeline (default)
                                        filter: start from raw TEs to the end.
                                        final: start from filtered TEs to finalizing the run.
                                        anno: perform whole-genome annotation/analysis after
                                                TE library construction.
        --overwrite [0|1]       If previous raw TE results are found, decide to overwrite
                                (1, rerun) or not (0, default).
        --cds [File]    Provide a FASTA file containing the coding sequence (no introns,
                        UTRs, nor TEs) of this genome or its close relative.
        --curatedlib [File]     Provided a curated library to keep consistant naming and
                                classification for known TEs. TEs in this file will be
                                trusted 100%, so please ONLY provide MANUALLY CURATED ones.
                                This option is not mandatory. It's totally OK if no file is
                                provided (default).
        --rmlib [File]  Provide the RepeatModeler library containing classified TEs to enhance
                        the sensitivity especially for LINEs. If no file is provided (default),
                        EDTA will generate such file for you.
        --sensitive [0|1]       Use RepeatModeler to identify remaining TEs (1) or not (0,
                                default). This step may help to recover some TEs.
        --anno [0|1]    Perform (1) or not perform (0, default) whole-genome TE annotation
                        after TE library construction.
        --rmout [File]  Provide your own homology-based TE annotation instead of using the
                        EDTA library for masking. File is in RepeatMasker .out format. This
                        file will be merged with the structural-based TE annotation. (--anno 1
                        required). Default: use the EDTA library for annotation.
        --maxdiv [0-100]        Maximum divergence (0-100%, default: 40) of repeat fragments comparing to
                                library sequences.
        --evaluate [0|1]        Evaluate (1) classification consistency of the TE annotation.
                                (--anno 1 required). Default: 1.
        --exclude [File]        Exclude regions (bed format) from TE masking in the MAKER.masked
                                output. Default: undef. (--anno 1 required).
        --force [0|1]   When no confident TE candidates are found: 0, interrupt and exit
                        (default); 1, use rice TEs to continue.
        --u [float]     Neutral mutation rate to calculate the age of intact LTR elements.
                        Intact LTR age is found in this file: *EDTA_raw/LTR/*.pass.list.
                        Default: 1.3e-8 (per bp per year, from rice).
        --repeatmodeler [path]  The directory containing RepeatModeler (default: read from ENV)
        --repeatmasker  [path]  The directory containing RepeatMasker (default: read from ENV)
        --annosine      [path]  The directory containing AnnoSINE_v2 (default: read from ENV)
        --ltrretriever  [path]  The directory containing LTR_retriever (default: read from ENV)
        --check_dependencies Check if dependencies are fullfiled and quit
        --threads|-t [int]      Number of theads to run this script (default: 4)
        --debug  [0|1]  Retain intermediate files (default: 0)
        --help|-h       Display this help info

运行后发现LTR鉴定过程报错

Mon Aug  5 16:34:45 CST 2024    Obtain raw TE libraries using various structure-based programs:
Mon Aug  5 16:34:46 CST 2024    EDTA_raw: Check dependencies, prepare working directories.

Mon Aug  5 16:34:53 CST 2024    Start to find LTR candidates.

Mon Aug  5 16:34:53 CST 2024    Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/x/miniconda3/envs/EDTA1/share/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 384.
cp: cannot stat '0712.390m.last.fasta.mod.retriever.scn.adj': No such file or directory
awk: fatal: cannot open file `0712.390m.last.fasta.mod.pass.list' for reading: No such file or directory
Warning: LOC list - is empty.

Error: Error while loading sequence
Filter sequence based on TEsorter classifications. Unclassified sequences will also be output to the clean file.
        Usage: perl cleanup_misclas.pl sequence.fa.rexdb.cls.tsv
        Author: Shujun Ou (shujun.ou.1@gmail.com) 10/11/2019

mv: cannot stat '0712.390m.last.fasta.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory
mv: cannot stat '0712.390m.last.fasta.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory
cp: cannot stat '0712.390m.last.fasta.mod.LTR.intact.raw.fa.anno.list': No such file or directory
ERROR: No such file or directory at /home/x/miniconda3/envs/EDTA1/share/EDTA/util/output_by_list.pl line 39.

        perl filter_gff3.pl file.gff3 file.list > new.gff3

Mon Aug  5 16:40:01 CST 2024    Warning: The LTR result file has 0 bp!

github搜索，发现问题与LTR_retriever有关，遂指定LTR_retriever路径，报错相同。
改变思路，使用docker运行程序，这一步的性能消耗不高，400m的基因组，30G内存足矣，分12线程也能很快跑完。

https://quay.io/repository/biocontainers/edta?tab=tags #找到最新的容器，下载
#我是在win下运行的，下载好tar之后导入镜像。本来看着很小只有2g，导出tar还挺大的，7.12G
Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
-a----          2024/8/6     17:08     7655989248 quay.io_biocontainers_edta_2.2.0--hdfd78af_1.tar
-a----          2024/8/2     14:50           8215 新建 文本文档.txt
docker load quay.io_biocontainers_edta_2.2.0--hdfd78af_1.tar
PS D:\bio_data\genome_make> docker run -v ${PWD}:/in -w /in quay.io/biocontainers/edta:2.2.0--hdfd78af_1 EDTA.pl --genome ./0712.400m.last.fasta -t 12
#正常运行
#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0  #####
##### Shujun Ou (shujun.ou.1@gmail.com)             #####
#########################################################


Parameters: --genome ./0712.400m.last.fasta -t 12


Tue Aug  6 09:24:29 UTC 2024    Dependency checking:
                                All passed!

Tue Aug  6 09:25:43 UTC 2024    Obtain raw TE libraries using various structure-based programs:
Tue Aug  6 09:25:43 UTC 2024    EDTA_raw: Check dependencies, prepare working directories.

Tue Aug  6 09:26:33 UTC 2024    Start to find LTR candidates.

Tue Aug  6 09:26:33 UTC 2024    Identify LTR retrotransposon candidates from scratch.

Tue Aug  6 09:34:51 UTC 2024    Finish finding LTR candidates.

Tue Aug  6 09:34:51 UTC 2024    Start to find SINE candidates.

从任务管理器可以看到峰值内存占用约20G。正常运行。不用跟conda搏斗的感觉真是太好了。