Testing output

[G-Thomson]

Hi

This looks like a very useful tool.

What is the expected output from the testing data?

I have installed EDTA v2.2.0 via conda since when I try to use the yml file I get errors to do with CUDA when I try to install tensorflow

​conda create -n edta python=3.10.12 edta=2.2.0 numpy pandas matplotlib jupyter cudatoolkit=11.8.0

When I run the test data I get an error for LTR.identifier.pl and SINE's and LINES's have 0bp. Is this expected?

Alternatively would it be possible to make a docker/singularity container for EDTA v2.2.0? as the most recent is EDTA v2.0.0

Parameters: --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice7.0.0.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --threads 10


Thu Feb  8 10:29:29 EST 2024	Dependency checking:

				All passed!

	A custom library ../database/rice7.0.0.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.

Thu Feb  8 10:29:33 EST 2024	Obtain raw TE libraries using various structure-based programs: 
Thu Feb  8 10:29:33 EST 2024	EDTA_raw: Check dependencies, prepare working directories.

Thu Feb  8 10:29:34 EST 2024	Start to find LTR candidates.

Thu Feb  8 10:29:34 EST 2024	Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at /home/got3/.conda/envs/edta2_2attempt2/share/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 11.
cp: cannot stat 'genome.fa.mod.retriever.scn.adj': No such file or directory
awk: fatal: cannot open file `genome.fa.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 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory
mv: cannot stat 'genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fa.mod.LTR.intact.raw.fa.anno.list': No such file or directory
ERROR: No such file or directory at /vast/palmer/scratch/jacob/got3/EDTA/util/output_by_list.pl line 39.

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

Thu Feb  8 10:29:49 EST 2024	Warning: The LTR result file has 0 bp!

Thu Feb  8 10:29:49 EST 2024	Start to find SINE candidates.

Thu Feb  8 10:31:15 EST 2024	Warning: The SINE result file has 0 bp!

Thu Feb  8 10:31:15 EST 2024	Start to find LINE candidates.

Thu Feb  8 10:31:15 EST 2024	Identify LINE retrotransposon candidates from scratch.

Thu Feb  8 10:33:16 EST 2024	Warning: The LINE result file has 0 bp!

Thu Feb  8 10:33:16 EST 2024	Start to find TIR candidates.

Thu Feb  8 10:33:16 EST 2024	Identify TIR candidates from scratch.

Species: others
Thu Feb  8 10:35:19 EST 2024	Finish finding TIR candidates.

Thu Feb  8 10:35:19 EST 2024	Start to find Helitron candidates.

Thu Feb  8 10:35:19 EST 2024	Identify Helitron candidates from scratch.

Thu Feb  8 10:35:52 EST 2024	Finish finding Helitron candidates.

Thu Feb  8 10:35:52 EST 2024	Execution of EDTA_raw.pl is finished!

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

​

[oushujun]

Hello,

Sorry for the delay response. Please update your repo and try with the updated yml file. It should be able to install without the CUDA dependency.

Best,
Shujun

[rpetroll]

Hi Shujun,

I am also getting the same error as described above. I also tried using the updated yml file, but still getting the same error and 0 Bp files for LINEs and SINEs. I also tried the container 2.2.0--hdfd78af_1, also here it is the same error.

I am very thankful for any advice.
Thank you!
Romy

[oushujun]

You can use the following mamba command to install EDTA:
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython 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-cpu==2.11 tesorter samtools bedtools grep

The bioconda and docker/singularity version is not yet updated. As EDTA2 is actively being developed, it's good to pull the github every while to get the latest version.

Thanks!
Shujun

[Mosy135]

Encountered same error, mamba install version failed in testing. Cloned git repository together with this env works fine
mamba create -n EDTA2.2 -c conda-forge -c bioconda -c r annosine2 biopython 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-cpu==2.11 tesorter samtools bedtools grep