Missing Header in dbcan-sub output

cristianrohr commented 5 months ago

Hello @linnabrown I have the output for the v4 of the dbcan software generated using this command

docker run -v ~/cazymes/data_db_rwll:/rwll -it dbcan:latest /rwll/run1.faa protein --out_dir /rwll/out1

But the dbcan-sub.hmm.out doesn't have a header

Can you provide the name of each column?

Thanks in advance

linnabrown commented 5 months ago

Hi @cristianrohr , thank you for using our tool. Current version of dbcan v4.1.4 provided header. You seems using a docker image. Did you build this tool from Dockerfile we provided or the docker image pulled down from Docker website?

cristianrohr commented 5 months ago

I build the docker image from this repo. Pulling the image from the docker website downloads an old 3.X version

I have run a very large dataset, if you can provide me with the header line I can use this data, instead of running everything again

Thanks in advance

linnabrown commented 5 months ago

@cristianrohr Got it. Current run_dbcan docker iamge is the old version. We will update the docker image and I will write a trigger to update docker image automatically. In stead, could you please use the conda version currently? Which is 4.1.4 currently. Thank you so much!

cristianrohr commented 5 months ago

I downloaded the latest version of repo 4.1.4 and the output dbcan-sub.hmm.out still doesn't have the header.

Please provide me with the header line. I need this information ASAP

thank you

yinlabniu commented 5 months ago

Please see https://bcb.unl.edu/dbCAN_tutorial/dataset1-Carter2023/individual_assembly/Wet2014.dbCAN/dbcan-sub.hmm.out.

A lot of information can be found at https://dbcan.readthedocs.io/en/latest/user_guide/run_from_raw_reads.html#example-1-carter2023-dataset-2023-carter.

Yanbin

From: CRohr @.> Sent: Friday, February 2, 2024 1:22 PM To: linnabrown/run_dbcan @.> Cc: Subscribed @.***> Subject: Re: [linnabrown/run_dbcan] Missing Header in dbcan-sub output (Issue #160)

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I downloaded the latest version of repo 4.1.4 and the output dbcan-sub.hmm.out still doesn't have the header.

Please provide me with the header line. I need this information ASAP

thank you

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yinlabniu commented 5 months ago

https://dbcan.readthedocs.io/en/latest/user_guide/run_from_raw_reads.html#box-6-example-output-folder-content-of-run-dbcan-substrate-prediction

From: Yanbin Yin @.> Sent: Friday, February 2, 2024 1:33 PM To: linnabrown/run_dbcan @.>; linnabrown/run_dbcan @.> Cc: Subscribed @.> Subject: Re: [linnabrown/run_dbcan] Missing Header in dbcan-sub output (Issue #160)

Please see https://bcb.unl.edu/dbCAN_tutorial/dataset1-Carter2023/individual_assembly/Wet2014.dbCAN/dbcan-sub.hmm.out.

A lot of information can be found at https://dbcan.readthedocs.io/en/latest/user_guide/run_from_raw_reads.html#example-1-carter2023-dataset-2023-carter.

Yanbin

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I downloaded the latest version of repo 4.1.4 and the output dbcan-sub.hmm.out still doesn't have the header.

Please provide me with the header line. I need this information ASAP

thank you

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linnabrown commented 5 months ago

I downloaded the latest version of repo 4.1.4 and the output dbcan-sub.hmm.out still doesn't have the header.

Please provide me with the header line. I need this information ASAP

thank you

Hi @cristianrohr , I have the header from dbcan-sub.hmm.out in 4.1.4 version of dbcan. Could you please confirm that whether you are using version 4.1.4?

linnabrown commented 5 months ago

Those are the headers:

dbCAN subfam Subfam Composition Subfam EC Substrate Profile Length Gene ID Gene Length E Value Profile Start Profile End Gene Start Gene End Coverage

Xinpeng021001 commented 5 months ago

I downloaded the latest version of repo 4.1.4 and the output dbcan-sub.hmm.out still doesn't have the header.

Please provide me with the header line. I need this information ASAP

thank you

Hi, I just run the dbCAN(v4.1.4) with dbCAN-sub and it shows the header in my result

Maybe you could re-install the dbCAN and check it again.

cristianrohr commented 5 months ago

I have downloaded this file https://github.com/linnabrown/run_dbcan/releases/download/4.1.4/dbcan-4.1.4.tar.gz Build the Dockerfile inside; and run the analysis with this command

docker run -v /data/proyectos/XX/cazymes/data_db_XX:/rewell -it dbcan4:latest /XX/run1.faa protein --out_dir /XX/salida1nuevo

And the header is missing,

I'll repeat the steps again

linnabrown / run_dbcan

Missing Header in dbcan-sub output #160