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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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braker3 - no etp_release.pl #565

Closed Thamos closed 1 year ago

Thamos commented 1 year ago

Hi, when running braker3 I had the error that "etp_release.pl" wasn't anywhere to be found in GeneMark-ETP/bin/ and so the tests (test1.sh, test2.sh, test3.sh) didn't work. I downloaded GeneMark-ETP from https://github.com/gatech-genemark/GeneMark-ETP

I think I solved the problem by creating a symbolic link of the script gmetp.pl, naming it etp_release.pl. It's running now with real data and I'm eagerly awaiting the first results. :)

If somebody else has problems running braker3 I recommed also looking at my issue at GeneMark-ETP https://github.com/gatech-genemark/GeneMark-ETP/issues/1

KatharinaHoff commented 1 year ago

The problem is that you need GeneMark-ETP. It is not available at http://topaz.gatech.edu/genemark/license_download.cgi at the moment. You have to wait until it is available.

Thamos @.***> schrieb am Mi. 18. Jan. 2023 um 00:26:

Hi, when running braker3 I had the error that "etp_release.pl" wasn't anywhere to be found in GeneMark-ETP/bin/ and so the tests (test1.sh, test2.sh, test3.sh) didn't work. I downloaded GeneMark-ETP from https://github.com/gatech-genemark/GeneMark-ETP

I think I solved the problem by creating a symbolic link of the script gmetp.pl, naming it etp_release.pl. It's running now with real data and I'm eagerly awaiting the first results. :)

If somebody else has problems running braker3 I recommed also looking at my issue at GeneMark-ETP gatech-genemark/GeneMark-ETP#1 https://github.com/gatech-genemark/GeneMark-ETP/issues/1

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Thamos commented 1 year ago

Readme says

"Download GeneMark-ETP from https://github.com/gatech-genemark/GeneMark-ETP or https://topaz.gatech.edu/GeneMark/etp.for_braker.tar.gz. Unpack and install GeneMark-ETP as described in GeneMark-ETP’s README file."

so that's why I downloaded it from github. Anyway with the changes tests ran successfully now and I'm trying with real data.

KatharinaHoff commented 1 year ago

Then we need to change the docs probably. @LarsGab we are apparently providing conflicting information?

Thamos commented 1 year ago

Is there a reason to not use the version on github? Because if e.g. there are problems with the results I'll cancel the run and won't use braker3 for now.

KatharinaHoff commented 1 year ago

We are not sure. I was not allowed to put it into the container because they said sth was not optimal with the code. Unless sth changed on Github during PAG.

Thamos @.***> schrieb am Mi. 18. Jan. 2023 um 02:40:

Is there a reason to not use the version on github? Because if e.g. there are problems with the results I'll cancel the run and won't use braker3 for now.

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KatharinaHoff commented 1 year ago

Ok, they did change sth. Maybe that’s what they will release. I am not at PAG, so nobody told me. We will adapt documentation.

Katharina Hoff @.***> schrieb am Mi. 18. Jan. 2023 um 02:43:

We are not sure. I was not allowed to put it into the container because they said sth was not optimal with the code. Unless sth changed on Github during PAG.

Thamos @.***> schrieb am Mi. 18. Jan. 2023 um 02:40:

Is there a reason to not use the version on github? Because if e.g. there are problems with the results I'll cancel the run and won't use braker3 for now.

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Thamos commented 1 year ago

Ah well then I will just let it run and check when it's finished or there's an error. Btw really nice that there's the container now. I remember setting up braker2 took a bit of time, now it's just one command :)

kashiff007 commented 1 year ago

Hi Braker3 Team, I am trying to use the braker3 but facing the problem of missing file etp_release.pl. I am also unable to find this file in https://github.com/gatech-genemark/GeneMark-ETP.

I am wondering the braker3 is available to use?

KatharinaHoff commented 1 year ago

Regrettably we all need to remain patient. ETP availability is out of our hands. Hang in there and wait with us…

Kashif Nawaz @.***> schrieb am Di. 31. Jan. 2023 um 14:40:

Hi Braker3 Team, I am trying to use the braker3 but facing the problem of missing file etp_release.pl. I am also unable to find this file in https://github.com/gatech-genemark/GeneMark-ETP.

I am wondering the braker3 is available to use?

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Thamos commented 1 year ago

@kashiff007 Just do what I described in the first post of this issue, the etp repository didn't get changed except for bugfixes. So in commands it would be "ln -s gmetp.pl etp_release.pl" from inside the etp bin folder.

kashiff007 commented 1 year ago

@Thamos, its working. Thank you

KatharinaHoff commented 1 year ago

It is currently NOT working properly (as expected) for larger genomes. That’s why we are waiting for a fix on the ETP side.

Kashif Nawaz @.***> schrieb am Mi. 1. Feb. 2023 um 08:12:

@Thamos https://github.com/Thamos, its working. Thank you

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kashiff007 commented 1 year ago

@KatharinaHoff Thanks for the clarification. I am running multiple annotators and will compare them.

sqwwww commented 1 year ago

Hi, I am trying to use the braker3 and met the same problem, I download GeneMark-ES/ET/EP ver 4.71_lic from http://topaz.gatech.edu/GeneMark/license_download.cgi, there is no etp_release.pl, and no gmetp.pl mentioned above. Is there a way to figure it out? I show what I have download in the picture. image

mericl commented 1 year ago

I have the exact same issue "# WARNING: Couldn't find" after following the directions to "git clone https://github.com/gatech-genemark/GeneMark-ETP.git" and setting my ETP path correctly (using both $GENEMARK_PATH and $ETP), is there any update on this issue?

sqwwww commented 1 year ago

I have the exact same issue "# WARNING: Couldn't find" after following the directions to "git clone https://github.com/gatech-genemark/GeneMark-ETP.git" and setting my ETP path correctly (using both $GENEMARK_PATH and $ETP), is there any update on this issue?

I'm also confused about it, it seems that GeneMark changed a lot, and braker doesn't adapt to the new changes. I turned to funannotate and some other tools for gene annotation.

KatharinaHoff commented 1 year ago

Some of us are out of office. You need to wait until we are back. Sorry. Update will definitely happen.

sqwwww @.***> schrieb am Fr. 24. Feb. 2023 um 03:59:

I have the exact same issue "# WARNING: Couldn't find" after following the directions to "git clone https://github.com/gatech-genemark/GeneMark-ETP.git" and setting my ETP path correctly (using both $GENEMARK_PATH and $ETP), is there any update on this issue?

I'm also confused about it, it seems that GeneMark changed a lot, and braker doesn't adapt to the new changes. I turned to funannotate and some other tools for gene annotation.

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KatharinaHoff commented 1 year ago

The container has today been updated to contain GeneMark-ETP. You still have to install the license key file in your home directory (license key of GeneMark-ES/ET/EP works) as file ~/.gm_key. Otherwise, it should be very easy to run, now.

KatharinaHoff commented 1 year ago

No.

Thamos @.***> schrieb am Do. 2. März 2023 um 20:20:

Are the dependencies for UTR prediciton included too? I think in the last version they weren't.

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