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hoonjeseong / acr

Additional Clustering Refiner
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GeneMark-ES Path Error #2

Open jbh2313 opened 2 months ago

jbh2313 commented 2 months ago

Hello,

I am trying to use ACR. I have installed all of the necessary dependencies in a Conda environment, and I'm trying to run it on some test data with --target set to both. When I leave the programs.txt file alone (the way it is by default), ACR will get through about 2-3 bins before it exits with the error:

 ERROR:root:an error occured while executing eukrep ['/path/to/EukRep', '-i', '/path/to/bin_fasta/bin.44.fa', '-o', '/path/to/eukrep.tmp', '-ff']

If I instead try to change the programs.txt path to my installation of GeneMark-ES, ACR exits immediately with the error:

ERROR:root:Please set the [absolute/path/to/gmes_linux_64] path !

I installed GeneMark-ES version 4.72 from the link on this repo. I'm not sure if I'm supposed to set the path to the base gmes directory, or one of the scripts in that directory (which I'm assuming could be gmes_petap.pl, gmhmme3, or run_es.pl). I tried setting the path to those 3 scripts and they all gave the same error. Do you have any idea what could cause these errors and how to fix it?

hoonjeseong commented 2 months ago

Hi Jordan,

Sorry for the late reply, and thanks for the detailed description. I'll look closer and get back to you with a solution soon. Or have you ever used Docker? I've created a Docker image to minimize errors, and you can use it without installing anything. I haven't uploaded it to GitHub yet, but I'd like to share it with you. What do you think?

Best, Hoon Je

On Sun, Aug 25, 2024 at 4:05 AM Jordan Hernandez @.***> wrote:

Hello,

I am trying to use ACR. I have installed all of the necessary dependencies in a Conda environment, and I'm trying to run it on some test data with --target set to both. When I leave the programs.txt file alone (the way it is by default), ACR will get through about 2-3 bins before it exits with the error:

ERROR:root:an error occured while executing eukrep ['/path/to/EukRep', '-i', '/path/to/bin_fasta/bin.44.fa', '-o', '/path/to/eukrep.tmp', '-ff']

If I instead try to change the programs.txt path to my installation of GeneMark-ES, ACR exits immediately with the error:

ERROR:root:Please set the [absolute/path/to/gmes_linux_64] path !

I installed GeneMark-ES version 4.72 from the link on this repo. I'm not sure if I'm supposed to set the path to the base gmes directory, or one of the scripts in that directory (which I'm assuming could be gmes_petap.pl, gmhmme3, or run_es.pl). I tried setting the path to those 3 scripts and they all gave the same error. Do you have any idea what could cause these errors and how to fix it?

— Reply to this email directly, view it on GitHub https://github.com/hoonjeseong/acr/issues/2, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJNPKUGH2ELQDBRVDFT7NOTZTDKQVAVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DIOBQG4YDIOA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Hoon Je Seong, Ph.D.

Senior Researcher Korean Medicine Data Division Korea Institute of Oriental Medicine Office Tel: 042-868-9295 Email: @./ @.

jbh2313 commented 2 months ago

Hi Hoon Je,

I have a little experience with Docker, at least enough to run code from a pre-built image. Does the image include all the dependencies of ACR, including GeneMark-ES and the repository itself? If so, then the Docker image would definitely be helpful, and would eliminate the need to manually clone the repo myself. Thank you for offering to share it.

Regards, Jordan

Jordan B. Hernandez PhD Candidate University of Nebraska Medical Center

From: Hoon Je @.> Date: Wednesday, August 28, 2024 at 9:59 AM To: hoonjeseong/acr @.> Cc: Hernandez, Jordan B @.>, Author @.> Subject: Re: [hoonjeseong/acr] GeneMark-ES Path Error (Issue #2) Non-UNMC email Hi Jordan, Sorry for the late reply, and thanks for the detailed description. I'll look closer and get back to you with a solution soon. Or have you ever used Docker? I've created a Docker image to minimize errors, and you can use it

Hi Jordan,

Sorry for the late reply, and thanks for the detailed description. I'll look closer and get back to you with a solution soon. Or have you ever used Docker? I've created a Docker image to minimize errors, and you can use it without installing anything. I haven't uploaded it to GitHub yet, but I'd like to share it with you. What do you think?

Best, Hoon Je

On Sun, Aug 25, 2024 at 4:05 AM Jordan Hernandez @.***> wrote:

Hello,

I am trying to use ACR. I have installed all of the necessary dependencies in a Conda environment, and I'm trying to run it on some test data with --target set to both. When I leave the programs.txt file alone (the way it is by default), ACR will get through about 2-3 bins before it exits with the error:

ERROR:root:an error occured while executing eukrep ['/path/to/EukRep', '-i', '/path/to/bin_fasta/bin.44.fa', '-o', '/path/to/eukrep.tmp', '-ff']

If I instead try to change the programs.txt path to my installation of GeneMark-ES, ACR exits immediately with the error:

ERROR:root:Please set the [absolute/path/to/gmes_linux_64] path !

I installed GeneMark-ES version 4.72 from the link on this repo. I'm not sure if I'm supposed to set the path to the base gmes directory, or one of the scripts in that directory (which I'm assuming could be gmes_petap.pl, gmhmme3, or run_es.pl). I tried setting the path to those 3 scripts and they all gave the same error. Do you have any idea what could cause these errors and how to fix it?

— Reply to this email directly, view it on GitHub https://github.com/hoonjeseong/acr/issues/2 [github.com]https://urldefense.com/v3/__https:/github.com/hoonjeseong/acr/issues/2*3E__;JQ!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9YCPcDR4A$, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJNPKUGH2ELQDBRVDFT7NOTZTDKQVAVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DIOBQG4YDIOA [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AJNPKUGH2ELQDBRVDFT7NOTZTDKQVAVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DIOBQG4YDIOA*3E__;JQ!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9YMF7Eg9Y$ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Hoon Je Seong, Ph.D.

Senior Researcher Korean Medicine Data Division Korea Institute of Oriental Medicine Office Tel: 042-868-9295 Email: @./ @.

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/hoonjeseong/acr/issues/2*issuecomment-2315605334__;Iw!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9Y2aexmWk$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/ATH652LLXFPUUKSFUWTD3OTZTXQT3AVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJVGYYDKMZTGQ__;!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9YOFzh-4I$. You are receiving this because you authored the thread.Message ID: @.***>

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hoonjeseong commented 2 months ago

Hi,

Here's the docker image link (https://hub.docker.com/r/hoonje/acr).

There are some caveats to using it.

  1. The genemark-es program requires a license every few months, so you must get it personally and include it when running the ACR container. -> http://exon.gatech.edu/GeneMark/license_download.cgi (select GeneMark-ES/ET/EP and linux 64-> you can get the gm_key_64)
    1. Due to the size of the image, I uploaded the db separately, so please get the db as well and include it when running the ACR container. -> wget -O data.tar.gz https://figshare.com/ndownloader/files/41282157 && tar -zxvf data.tar.gz -> you can get the data folder (DB)

Here is an example of an executable command that includes them. -docker cmd: docker run --rm -v [downloaded DB folder]:/acr/data -v [path of 'gm_key_64'] :/root/.gm_key -v [Folders with data to input and output]:/data/hoonje/acr:0.2.1 acr.py -g /data/test_SHIPPO -o /data/output_SHIPPO -c /data/test_SHIPPO/cov.txt (ACR command. you can get test dataset in the github: hoonjeseong/acr: Additional Clustering Refiner (github.com) https://github.com/hoonjeseong/acr)

Please test with a test dataset again.

Best, Hoon Je

I attached the email capture because the GitHub reply system removes the color in the text. image

On Thu, Aug 29, 2024 at 2:02 AM Jordan Hernandez @.***> wrote:

Hi Hoon Je,

I have a little experience with Docker, at least enough to run code from a pre-built image. Does the image include all the dependencies of ACR, including GeneMark-ES and the repository itself? If so, then the Docker image would definitely be helpful, and would eliminate the need to manually clone the repo myself. Thank you for offering to share it.

Regards, Jordan

Jordan B. Hernandez PhD Candidate University of Nebraska Medical Center

From: Hoon Je @.> Date: Wednesday, August 28, 2024 at 9:59 AM To: hoonjeseong/acr @.> Cc: Hernandez, Jordan B @.>, Author @.> Subject: Re: [hoonjeseong/acr] GeneMark-ES Path Error (Issue #2) Non-UNMC email Hi Jordan, Sorry for the late reply, and thanks for the detailed description. I'll look closer and get back to you with a solution soon. Or have you ever used Docker? I've created a Docker image to minimize errors, and you can use it

Hi Jordan,

Sorry for the late reply, and thanks for the detailed description. I'll look closer and get back to you with a solution soon. Or have you ever used Docker? I've created a Docker image to minimize errors, and you can use it without installing anything. I haven't uploaded it to GitHub yet, but I'd like to share it with you. What do you think?

Best, Hoon Je

On Sun, Aug 25, 2024 at 4:05 AM Jordan Hernandez @.***> wrote:

Hello,

I am trying to use ACR. I have installed all of the necessary dependencies in a Conda environment, and I'm trying to run it on some test data with --target set to both. When I leave the programs.txt file alone (the way it is by default), ACR will get through about 2-3 bins before it exits with the error:

ERROR:root:an error occured while executing eukrep ['/path/to/EukRep', '-i', '/path/to/bin_fasta/bin.44.fa', '-o', '/path/to/eukrep.tmp', '-ff']

If I instead try to change the programs.txt path to my installation of GeneMark-ES, ACR exits immediately with the error:

ERROR:root:Please set the [absolute/path/to/gmes_linux_64] path !

I installed GeneMark-ES version 4.72 from the link on this repo. I'm not sure if I'm supposed to set the path to the base gmes directory, or one of the scripts in that directory (which I'm assuming could be gmes_petap.pl,

gmhmme3, or run_es.pl). I tried setting the path to those 3 scripts and they all gave the same error. Do you have any idea what could cause these errors and how to fix it?

— Reply to this email directly, view it on GitHub https://github.com/hoonjeseong/acr/issues/2 [github.com]< https://urldefense.com/v3/__https:/github.com/hoonjeseong/acr/issues/2*3E__;JQ!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9YCPcDR4A$>, or unsubscribe < https://github.com/notifications/unsubscribe-auth/AJNPKUGH2ELQDBRVDFT7NOTZTDKQVAVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DIOBQG4YDIOA> [github.com]< https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/AJNPKUGH2ELQDBRVDFT7NOTZTDKQVAVCNFSM6AAAAABNB2KOV6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DIOBQG4YDIOA*3E__;JQ!!JkUDQA!OwvxSoTJH_5KtjZM1Zp-S4EOYGAWzElfzIoxH9vaUdUQKV4Fk9toiGTB1upAUYWByrbm23k9NJjm8F3GeF9VLx9YMF7Eg9Y$>

. You are receiving this because you are subscribed to this thread.Message ID: @.***>

-- Hoon Je Seong, Ph.D.

Senior Researcher Korean Medicine Data Division Korea Institute of Oriental Medicine Office Tel: 042-868-9295 Email: @./ @.

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Senior Researcher Korean Medicine Data Division Korea Institute of Oriental Medicine Office Tel: 042-868-9295 Email: @./ @.