ERROR: Intact TE annotation not found in Aros.genome.fa.mod.EDTA.intact.gff3 at EDTA.pl line 638.

[chun-he-316]

Hi,
I ran the command "perl ~/mambaforge/envs/EDTA/bin/EDTA.pl -genome Aros.genome.fa -t 56 -sensitive 1 -anno 1 --evaluate 1 --species others --force 1",but I met a problem. The error are as follows:
#########################################################

Extensive de-novo TE Annotator (EDTA) v2.2.0

Shujun Ou (shujun.ou.1@gmail.com)

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

Parameters: -genome Aros.genome.fa -t 56 -sensitive 1 -anno 1 --evaluate 1 --species others --force 1

Invalid value for shared scalar at /data/hechun/mambaforge/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 209.
cp: 'Aros.genome.fa.mod.retriever.scn.adj' is not available. status: no such file or directory
awk: cannot open Aros.genome.fa.mod.pass.list (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: 'Aros.genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln' is not available. status: no such file or directory
mv: 'Aros.genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list' is not available. status: no such file or directory
cp: 'Aros.genome.fa.mod.LTR.intact.raw.fa.anno.list' is not available. status: no such file or directory
ERROR: No such file or directory at /data/hechun/mambaforge/envs/EDTA/share/EDTA/util/output_by_list.pl line 39.

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

10:15:21 CST Warning: The LTR result file has 0 bp!
10:15:21 CST Start to find SINE candidates.

cp: 'Aros.genome.fa.mod.SINE.raw.fa' are not available. status: no such file or directory
Error: SINE results not found!

cat: Aros.genome.fa.mod.TIR.intact.raw.bed: no such file or directory
cat: Aros.genome.fa.mod.Helitron.intact.raw.bed: no such file or directory
10:15:21 CST Obtain raw TE libraries finished.
All intact TEs found by EDTA:
Aros.genome.fa.mod.EDTA.intact.raw.fa
Aros.genome.fa.mod.EDTA.intact.raw.gff3

10:15:21 CST Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library:
Warning: No repetitive sequences were detected in Aros.genome.fa.mod.SINE.raw.fa
10:34:09 CST EDTA advance filtering finished.
10:34:09 CST Perform EDTA final steps to generate a non-redundant comprehensive TE library.

cp: '../Aros.genome.fa.mod.EDTA.raw/Aros.genome.fa.mod.RM2.fa' are not available. status: no such file or directory
Skipping the RepeatModeler results (--sensitive 0).
Run EDTA.pl --step final --sensitive 1 if you want to add RepeatModeler results.

			Skipping the CDS cleaning step (--cds [File]) since no CDS file is provided or it's empty.

ERROR: Intact TE annotation not found in Aros.genome.fa.mod.EDTA.intact.gff3 at EDTA.pl line 638.

Please tell me how to resolve this problem. I really need your help. Thanks.

The best,
Chun

[oushujun]

Did you test EDTA on the test files? Seems like your genome is a special one. Shujun

…

On Mon, Mar 4, 2024 at 10:10 PM chun-he-316 ***@***.***> wrote: Hi, I ran the command "perl ~/mambaforge/envs/EDTA/bin/EDTA.pl -genome Aros.genome.fa -t 56 -sensitive 1 -anno 1 --evaluate 1 --species others --force 1",but I met a problem. The error are as follows: ######################################################### Extensive de-novo TE Annotator (EDTA) v2.2.0 Shujun Ou ( ***@***.***) ######################################################### Parameters: -genome Aros.genome.fa -t 56 -sensitive 1 -anno 1 --evaluate 1 --species others --force 1 Invalid value for shared scalar at /data/hechun/mambaforge/envs/EDTA/share/LTR_retriever/bin/ LTR.identifier.pl line 114, line 209. cp: 'Aros.genome.fa.mod.retriever.scn.adj' is not available. status: no such file or directory awk: cannot open Aros.genome.fa.mod.pass.list (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 ***@***.***) 10/11/2019 mv: 'Aros.genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln' is not available. status: no such file or directory mv: 'Aros.genome.fa.mod.LTR.intact.fa.ori.dusted.cln.cln.list' is not available. status: no such file or directory cp: 'Aros.genome.fa.mod.LTR.intact.raw.fa.anno.list' is not available. status: no such file or directory ERROR: No such file or directory at /data/hechun/mambaforge/envs/EDTA/share/EDTA/util/output_by_list.pl line 39. perl filter_gff3.pl file.gff3 file.list > new.gff3 10:15:21 CST Warning: The LTR result file has 0 bp! 10:15:21 CST Start to find SINE candidates. cp: 'Aros.genome.fa.mod.SINE.raw.fa' are not available. status: no such file or directory Error: SINE results not found! cat: Aros.genome.fa.mod.TIR.intact.raw.bed: no such file or directory cat: Aros.genome.fa.mod.Helitron.intact.raw.bed: no such file or directory 10:15:21 CST Obtain raw TE libraries finished. All intact TEs found by EDTA: Aros.genome.fa.mod.EDTA.intact.raw.fa Aros.genome.fa.mod.EDTA.intact.raw.gff3 10:15:21 CST Perform EDTA advance filtering for raw TE candidates and generate the stage 1 library: Warning: No repetitive sequences were detected in Aros.genome.fa.mod.SINE.raw.fa 10:34:09 CST EDTA advance filtering finished. 10:34:09 CST Perform EDTA final steps to generate a non-redundant comprehensive TE library. cp: '../Aros.genome.fa.mod.EDTA.raw/Aros.genome.fa.mod.RM2.fa' are not available. status: no such file or directory Skipping the RepeatModeler results (--sensitive 0). Run EDTA.pl --step final --sensitive 1 if you want to add RepeatModeler results. Skipping the CDS cleaning step (--cds [File]) since no CDS file is provided or it's empty. ERROR: Intact TE annotation not found in Aros.genome.fa.mod.EDTA.intact.gff3 at EDTA.pl line 638. Please tell me how to resolve this problem. I really need your help. Thanks. The best, Chun — Reply to this email directly, view it on GitHub <#441>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNX4NHMVT2P2772QBG2WETYWUZS5AVCNFSM6AAAAABEGKVS7OVHI2DSMVQWIX3LMV43ASLTON2WKOZSGE3DQMRQGIYDEMY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yanarizzieri]

Hello Shujun,

I was having the same issue even when using the test file (which suggests a problem with the installation). I tried a new env like you suggest in issues #429, but I was only able to have no erros when using EDTA version 2.0.1 (instead of 2.2)

Yana