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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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Fasta file issue #374

Closed Ramkyeri closed 5 months ago

Ramkyeri commented 11 months ago

Dear @oushujun

Many thanks for developing this very useful tool.

it is not accepting cds fasta file.

this is my file format

image

with regards

Ramky

oushujun commented 11 months ago

Hi Ramky,

Can you provide the error message here? Thanks

Shujun

oushujun commented 10 months ago

@Ramkyeri any luck?

Ramkyeri commented 10 months ago

Dear Shujun, Thank you for your message. I will update you soon. sorry for the delay.

with regards

Ramky

On Mon, Aug 21, 2023 at 4:32 AM Shujun Ou @.***> wrote:

@Ramkyeri https://github.com/Ramkyeri any luck?

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/374#issuecomment-1685391470, or unsubscribe https://github.com/notifications/unsubscribe-auth/AQ3Y3GU35P2L4IS5TXHNJWLXWJX5ZANCNFSM6AAAAAA26LIHPY . You are receiving this because you were mentioned.Message ID: @.***>

Ramkyeri commented 10 months ago

Dear Shujun, Greetings! Many thanks for your kindness. I am so sorry for the dealyed response.

This is the error:

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

Extensive de-novo TE Annotator (EDTA) v2.0.0
Shujun Ou (shujun.ou.1@gmail.com)

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

Sat Aug 26 02:59:05 UTC 2023 Dependency checking: All passed!

ERROR: The CDS file Phyllostachys_edulis_V1.cds you specified is not found!

with regards

Ramky

Ramkyeri commented 10 months ago

Dear Shujun, It is not accepting cds file, I donot know the reason, Now I am running without cds file using nohup command, I am using our server, after closing the terminal, EDTA is not running.

with regards Ramky

oushujun commented 10 months ago

Can you provide the command you used that has the error?

Ramkyeri commented 10 months ago

Dear Shujun,

This is the command

nohup singularity exec EDTA.sif EDTA.pl --genome genome.fa --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 25

with regards Ramky

oushujun commented 10 months ago

I see. There may be some issues of passing files to the container. You may want to use the conda version instead of docker/singularity.

Shujun

Ramkyeri commented 10 months ago

Dear Shujun,

Thank you, Conda version needs many dependencies.

with regards

Ramky

oushujun commented 10 months ago

Yup. They can be installed through: conda env create -f EDTA.yml

Shujun

Ramkyeri commented 10 months ago

Dear Shujun, Thank you for your kind response. I will update you further results. My genome is 1.9 GB in size. How long will the analysis take? with regards Ramky

Ramkyeri commented 9 months ago

Dear Shujun,

As per your suggestion, I used conda env create -f EDTA.yml,

I got the following while running the code,

perl ../EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10

gt is not found in the genometools path ./!

with regards

ramky

oushujun commented 9 months ago

Hi Ramky,

That means EDTA is not correctly installed. Please reinstall and try again.

Shujun

Ramkyeri commented 9 months ago

Dear Shujun, Thanks for your kind reply. I will update you. with regards

ramky

Ramkyeri commented 9 months ago

Dear Shujun,

I have re-installed EDTA.yml, interestingly conda environment accepted cds file, but singularity did not accept the cds file.

thank you I will update you the results.

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

Extensive de-novo TE Annotator (EDTA) v2.0.1
Shujun Ou (shujun.ou.1@gmail.com)

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

Thu Sep 14 02:45:50 AM UTC 2023 Dependency checking: All passed!

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

Thu Sep 14 02:46:05 AM UTC 2023 Obtain raw TE libraries using various structure-based programs: Thu Sep 14 02:46:05 AM UTC 2023 EDTA_raw: Check dependencies, prepare working directories.

Thu Sep 14 02:46:08 AM UTC 2023 Start to find LTR candidates.

Thu Sep 14 02:46:08 AM UTC 2023 Identify LTR retrotransposon candidates from scratch.

with regards ramky

Ramkyeri commented 7 months ago

Dear @oushujun

Thed EDTA is runing more than 45 days, now it is in slow step, I do not know how long it will take to complete this slow stop, but this is the last step.

with regards Ramky

oushujun commented 7 months ago

Which step exactly? The evaluation step is not necessary for annotation. Thanks!

Shujun

On Wed, Nov 15, 2023 at 5:54 AM Muthusamy Ramakrishnan < @.***> wrote:

Dear @oushujun https://github.com/oushujun

Thed EDTA is runing more than 45 days, now it is in slow step, I do not know how long it will take to complete this slow stop, but this is the last step.

with regards Ramky

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/374#issuecomment-1812264119, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NG227UETNZTF6UP253YESNMVAVCNFSM6AAAAAA26LIHP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJSGI3DIMJRHE . You are receiving this because you were mentioned.Message ID: @.***>

Ramkyeri commented 7 months ago

Dear @oushujun this step Wed Oct 4 01:23:37 PM UTC 2023 Evaluate the level of inconsistency for whole-genome TE annotation (slow step):

with regards Ramky

oushujun commented 7 months ago

Yes this is the evaluation step I mentioned

Shujun

On Fri, Nov 17, 2023 at 8:45 PM Muthusamy Ramakrishnan < @.***> wrote:

Dear @oushujun https://github.com/oushujun this step Wed Oct 4 01:23:37 PM UTC 2023 Evaluate the level of inconsistency for whole-genome TE annotation (slow step):

with regards Ramky

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/374#issuecomment-1817315622, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCFNGMYVOUYJOSK4X3YFAHJ5AVCNFSM6AAAAAA26LIHP2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJXGMYTKNRSGI . You are receiving this because you were mentioned.Message ID: @.***>

Ramkyeri commented 7 months ago

Dear @oushujun Thank you for your reply. So, I can just stop the program using Kill command.
with regards Ramky

Ramkyeri commented 7 months ago

Dear @oushujun

Finally it is completed,

Wed Oct 4 01:23:37 PM UTC 2023 Evaluate the level of inconsistency for whole-genome TE annotation (slow step):

Wed Nov 29 12:14:57 PM UTC 2023 Evaluation of TE annotation finished! Check out these files:

            Overall: sequence.fasta.mod.EDTA.TE.fa.stat.all.sum
            Nested: sequence.fasta.mod.EDTA.TE.fa.stat.nested.sum
            Non-nested: sequence.fasta.mod.EDTA.TE.fa.stat.redun.sum

Thank you for your support with regards Ramky