Warning: LOC list - is empty / NO LTRs, SINES or LINES

[keith-harrison]

Hi I am wondering if there is any error here. I have done TE predictions for like 8 genomes (around 20MB) in the same family and normally find a high number of TEs and find that this specific species does not have as good results as the rest.

/shared/EDTA/EDTA.pl --genome genome.fasta --overwrite 1 --sensitive 1 
--anno 1 --threads 6 --evaluate 1 --force 1

#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0  #####
##### Shujun Ou ([email protected])             #####
#########################################################


Parameters: --genome genome.fasta --overwrite 1 --sensitive 1 --anno 1 --threads 6 --evaluate 1 --force 1


Wed  5 Mar 15:14:07 GMT 2025    Dependency checking:
                                All passed!

Wed  5 Mar 15:14:08 GMT 2025    Obtain raw TE libraries using various structure-based programs: 
Wed  5 Mar 15:14:08 GMT 2025    EDTA_raw: Check dependencies, prepare working directories.

Wed  5 Mar 15:14:08 GMT 2025    Start to find LTR candidates.

Wed  5 Mar 15:14:08 GMT 2025    Identify LTR retrotransposon candidates from scratch.

awk: fatal: cannot open file `genome.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 ([email protected]) 10/11/2019

mv: cannot stat 'genome.fasta.mod.LTR.intact.fa.ori.dusted.cln.cln': No such file or directory
mv: cannot stat 'genome.fasta.mod.LTR.intact.fa.ori.dusted.cln.cln.list': No such file or directory
cp: cannot stat 'genome.fasta.mod.LTR.intact.raw.fa.anno.list': No such file or directory
ERROR: No such file or directory at /shared/EDTA/util/output_by_list.pl line 39.

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

Wed  5 Mar 15:14:20 GMT 2025    Warning: The LTR result file has 0 bp!

Wed  5 Mar 15:14:20 GMT 2025    Start to find SINE candidates.
.... Similar results follow from this.

Thanks,
Keith

[ryandkuster]

I'm getting nearly the same error using version v2.2.2 (quay.io-biocontainers-edta-2.2.2--hdfd78af_1 image via apptainer).
My error includes a cds input and has Error: cd-hit-est is not found in the CDHIT path ! even though the dependency check states All passed!. @keith-harrison are you using a containerized version of EDTA, by chance?

[asthaamishra]

@oushujun Hi, I have also installed version v2.2.2 and am using a singularity container (with docker://quay.io/biocontainers/edta:2.2.2--hdfd78af_1). I have the same error as well:
Error: cd-hit-est is not found in the CDHIT path !

[keith-harrison]

No I use the conda/mamba version which works well for me (redownloaded last week to get the new version finally 👍 ). Also the error I am having has nothing to do with the error you are having since they occur independently, mine is just down to no LTRs being found in some of my genomes :) try to make a new github issue just so its clear for the author of the tool.