Warning: LOC list - is empty

wangyangXie commented 1 month ago

2024年 07月 19日星期五 14:36:11 CST Dependency checking: All passed!

    A custom library /public/home/xiewangyang/database/TE_db/sine_line_base.fa is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.

2024年 07月 19日星期五 14:36:45 CST Obtain raw TE libraries using various structure-based programs: 2024年 07月 19日星期五 14:36:45 CST EDTA_raw: Check dependencies, prepare working directories.

2024年 07月 19日星期五 14:36:55 CST Start to find LTR candidates.

2024年 07月 19日星期五 14:36:55 CST Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /public/home/xiewangyang/software/miniconda3/envs/TE/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 6072. cp: 无法获取'D.odori.Chr.20240714.fasta.mod.retriever.scn.adj' 的文件状态(stat): 没有那个文件或目录 awk: 致命错误：cannot open file `D.odori.Chr.20240714.fasta.mod.pass.list' for reading: 没有那个文件或目录 Warning: LOC list - is empty.

Isoris commented 1 month ago

Ive got the same issue, any solution?

wangyangXie commented 1 month ago

Ive got the same issue, any solution?

Hasn't solved the problem yet.

FayeFang17 commented 1 month ago

May I ask how did you install EDTA?

Isoris commented 1 month ago

With Conda as indicated on the front page.

On Tue, Jul 23, 2024, 1:50 AM Faye (Ning) Fang @.***> wrote:

May I ask how did you install EDTA?

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/483#issuecomment-2243604917, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASYS5TFSY5IJ5T4B5NWL67LZNVH55AVCNFSM6AAAAABLEGTMCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBTGYYDIOJRG4 . You are receiving this because you commented.Message ID: @.***>

FayeFang17 commented 1 month ago

Sorry for the late reply. Currently Conda install have some problems, would you like to try: git clone https://github.com/oushujun/EDTA.git mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter

This installation method might work better.

Chenglin20170390 commented 4 weeks ago

Sorry for the late reply. Currently Conda install have some problems, would you like to try: git clone https://github.com/oushujun/EDTA.git mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython blast cd-hit coreutils genericrepeatfinder genometools-genometools glob2 h5py==3.9 keras==2.11 ltr_finder ltr_retriever mdust multiprocess muscle openjdk pandas perl perl-text-soundex pyarrow python r-base r-dplyr regex repeatmodeler r-ggplot2 r-here r-tidyr scikit-learn swifter tensorflow==2.11 tesorter

This installation method might work better.

Hi I used this recommended commands for installation of EDTA, however, its show errors bellow. Thanks in advance.

EDTA_raw.pl  --genome $sample.chr.fa --species others --type tir --threads $th --overwrite 1

Fri Aug  9 20:51:55 CST 2024    EDTA_raw: Check dependencies, prepare working directories.
Fri Aug  9 20:52:18 CST 2024    Start to find TIR candidates.
Fri Aug  9 20:52:18 CST 2024    Identify TIR candidates from scratch.
Species: others
/work/home/miniforge3/envs/EDTA/bin/gt tirvish: error: fopen(): cannot open file 'TIR-Learner-+-gt_index.prj': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /work/home/softwares/edta/EDTA/util/rename_tirlearner.pl line 19.
Warning: LOC list AE.H2.chr.fa.mod.TIR.ext30.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 'AE.H2.chr.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln': No such file or directory
cp: cannot stat 'AE.H2.chr.fa.mod.TIR.ext30.fa.pass.fa.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'AE.H2.chr.fa.mod.TIR.intact.raw.fa.anno.list': No such file or directory
Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory.
Warning: The TIR result file has 0 bp!

Fri Aug  9 20:56:17 CST 2024    Execution of EDTA_raw.pl is finished!

Isoris commented 5 days ago

any updates ? did you add the EDTA folder to path ?

oushujun / EDTA

Warning: LOC list - is empty #483