Error in test and installation issue

[eliasprim]

Hello Dr Ou,

I am raising this issue, because I got an error while I was trying to run the test example.

The error I got is the following: Error: LTR_retriever is not found in the LTR_retriever path ./!

Most probably it is an installation issue and I tried to install EDTA with both conda ways, "Quick installation using conda (Linux64)" and "Other ways to install with conda".

With the first way I did not face any issues, while in the second one I got this:

Solving environment: failed with initial frozen solve. Retrying with flexible solve. Solving environment: failed with repodata from current_repodata.json, will retry with nexy repodata source. Collecting package metadata (current_repodata.json): done

And after that there is an infinite loading.

Do you have any ideas what is going wrong?

Thank you in advance.

Kind regards,

Elias Primetis

[oushujun]

Hi Elias,

Please refer to other similar issues. for example #250.

Best, Shujun

[eliasprim]

Hi Dr Ou,

After a lot of my own research I managed to install EDTA, but when I try to run the test in order to understand how EDTA works I get the following errors:

########################################################

Extensive de-novo TE Annotator (EDTA) v2.0.1

Shujun Ou ([email protected])

########################################################

Wed 14 Sep 12:07:43 BST 2022 Dependency checking: All passed!

A custom library ../database/rice6.9.5.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.

A CDS file genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.

A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.

Wed 14 Sep 12:07:45 BST 2022 Obtain raw TE libraries using various structure-based programs: Wed 14 Sep 12:07:45 BST 2022 EDTA_raw: Check dependencies, prepare working directories.

Wed 14 Sep 12:07:46 BST 2022 Start to find LTR candidates.

Wed 14 Sep 12:07:46 BST 2022 Identify LTR retrotransposon candidates from scratch.

Warning: LOC list genome.fa.mod.ltrTE.veryfalse is empty. Wed 14 Sep 12:08:11 BST 2022 Finish finding LTR candidates.

Wed 14 Sep 12:08:11 BST 2022 Start to find TIR candidates.

Wed 14 Sep 12:08:11 BST 2022 Identify TIR candidates from scratch.

Species: others dirname: missing operand Try 'dirname --help' for more information. Can't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.fa: No such file or directory at /mnt/RAID/method/EDTA/util/rename_tirlearner.pl line 19. Warning: LOC list genome.fa.mod.TIR.ext30.list is empty.

Error: Error while loading sequenceCan't open ./TIR-Learner-Result/TIR-Learner_FinalAnn.gff3: No such file or directory. Warning: The TIR result file has 0 bp!

Wed 14 Sep 12:08:12 BST 2022 Start to find Helitron candidates.

Wed 14 Sep 12:08:12 BST 2022 Identify Helitron candidates from scratch.

Wed 14 Sep 12:08:36 BST 2022 Finish finding Helitron candidates.

Wed 14 Sep 12:08:36 BST 2022 Execution of EDTA_raw.pl is finished!

ERROR: Raw TIR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.TIR.raw.fa If you believe the program is working properly, this may be caused by the lack of intact TIRs in your genome. Consider to use the --force 1 parameter to overwrite this check

I have checked a lot of similar issues, but nothing worked.

Could you please help me with that?

Kind regards,

Elias

[oushujun]

Hi Elias,

The error suggests the installation is still not good. Did you install EDTA on a standalone conda env or shared with other packages? You may try to reinstall in a brandnew env. Also, you may try mamba(https://anaconda.org/conda-forge/mamba) which can resolve environment much quicker than conda.

Best, Shujun