oushujun
commented
3 months ago 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
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yanarizzieri
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.
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.
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