Rerun EDTA 2.2.0 with results from older version

[CongLiu37]

Hello,

I have run EDTA v2.0.0 on my animal genomes with such commands: singularity exec ~/EDTA.sif EDTA.pl --genome ${cat_genome.fa} --species others --step all --overwrite 0 --sensitive 0 --anno 0 --threads 64 I did not do the annotation because those small fragments were merged to fake scaffolds in order to reduce running time of TIR-learner.

Now I want to use EDTA v2.2.0 to take the improvement in LINE/SINE search and do the annotation. Is it possible to run the new EDTA v2.2.0 with the results I already have and the original genome assembly? Something like this: EDTA.pl --genome ${genome.fa} --species others --step all --overwrite 0 --sensitive 1 --anno 1 --threads 64 --cds ${cds.fna}

Also, just one minor idea, it would be great if EDTA can do some file cleaning after running. It is difficult to copy/move the large file tree from TIR-learner.

Sincerely,

Cong

[oushujun]

It’s better to rerun the whole program, and you don’t need to merge the small contigs since TIR-Learner has upgraded.

Shujun

On Tue, Jan 30, 2024 at 12:00 AM Cong Liu @.***> wrote:

Hello,

I have run EDTA v2.0.0 on my animal genomes with such commands: singularity exec ~/EDTA.sif EDTA.pl --genome ${cat_genome.fa} --species others --step all --overwrite 0 --sensitive 0 --anno 0 --threads 64 I did not do the annotation because those small fragments were merged to fake scaffolds in order to reduce running time of TIR-learner.

Now I want to use EDTA v2.2.0 to take the improvement in LINE/SINE search and do the annotation. Is it possible to run the new EDTA v2.2.0 with the results I already have and the original genome assembly? Something like this: EDTA.pl --genome ${genome.fa} --species others --step all --overwrite 0 --sensitive 1 --anno 1 --threads 64 --cds ${cds.fna}

Also, just one minor idea, it would be great if EDTA can do some file cleaning after running. It is difficult to copy/move the large file tree from TIR-learner.

Sincerely,

Cong

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[CongLiu37]

Thanks for your quick reply. I am wondering if there is a singularity container for EDTA v2.2.0? I tried 2.2.0--hdfd78af_1 and 2.2.0--hdfd78af_0 from https://quay.io/repository/biocontainers/edta?tab=tags, but seems they are crashed. Here is the error:

FATAL: could not open image /apps/unit/BourguignonU/EDTA.sif: SIF image /hpcshare/appsunit/BourguignonU/EDTA.sif is corrupted: wrong partition size

Sincerely,

Cong

[GallVp]

Hi @CongLiu37

How did you build the singularity image? Can you kindly share your bash commands?

[CongLiu37]

Hello @GallVp

Here is the commands: singularity pull EDTA.sif docker://quay.io/biocontainers/edta:2.2.0--hdfd78af_1 The sif file was about 1.8G. Then I tried singularity exec EDTA.sif EDTA.pl --help and got the error: FATAL: could not open image /apps/unit/BourguignonU/EDTA.sif: SIF image /hpcshare/appsunit/BourguignonU/EDTA.sif is corrupted: wrong partition size

Sincerely,

Cong

[GallVp]

I am using docker and the file is about 8 GB. Anyways, can you try:

singularity pull EDTA.sif quay.io/biocontainers/edta:2.2.0--hdfd78af_1

If that does not work, simply download the build container from galaxy.

curl -LJO https://depot.galaxyproject.org/singularity/edta:2.2.0--hdfd78af_1

After download you can rename the file to EDTA.sif

[oushujun]

The current conda recipe is not correctly configured, so the docker/singularity derived from it won’t work. We are working on the conda recipe now.

Shujun

On Tue, Jan 30, 2024 at 5:44 PM Usman Rashid @.***> wrote:

I am using docker and the file is about 8 GB. Anyways, can you try:

singularity pull EDTA.sif quay.io/biocontainers/edta:2.2.0--hdfd78af_1

If that does not work, simply download the build container from galaxy.

curl -LJO https://depot.galaxyproject.org/singularity/edta:2.2.0--hdfd78af_1

After download you can rename the file to EDTA.sif

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/423#issuecomment-1918037989, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NCN4Q2RHSYHWSPWCDTYRFZV5AVCNFSM6AAAAABCQSX6BKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJYGAZTOOJYHE . You are receiving this because you commented.Message ID: @.***>

[CongLiu37]

Hello @oushujun @GallVp

Thanks for your messages. The curl command worked as singularity exec EDTA.sif EDTA.pl -h printed the help manual. But for the test: singularity exec /apps/unit/BourguignonU/EDTA.sif 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 there was something wrong with the dependencies:

perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
    LANGUAGE = (unset),
    LC_ALL = (unset),
    LANG = "en_GB.UTF-8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").

#########################################################
##### Extensive de-novo TE Annotator (EDTA) v2.2.0  #####
##### Shujun Ou (shujun.ou.1@gmail.com)             #####
#########################################################

Parameters: --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

Wed Jan 31 10:39:07 JST 2024    Dependency checking:
Error: gt is not found in the genometools path ./!

I am not sure about singularity, but I have gt installed:

which gt
~/miniconda3/bin/gt

Sincerely,

Cong

[CongLiu37]

Anyway I successfully installed all dependencies with mamba. Although I am still having issues, but it is in another question. I am closing this one. Thanks for your help.

Sincerely,

Cong