Missing Header in dbcan-sub output

[cristianrohr]

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]

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]

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]

@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]

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]

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) Caution: Non-NU Email 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 — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/linnabrown/run_dbcan/issues/160*issuecomment-1924534106__;Iw!!PvXuogZ4sRB2p-tU!FrZjeE76JdRvt7hAVFgWspBl1k0aD06sNdYqA1GdoFWKK20LhMjw7ZzG1QGpaHuHaJKtvpzfOyyTVj1jej2_4Q$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEXNKZQIG3Q6MIZCSITKJFTYRU4I3AVCNFSM6AAAAABCPM5GFGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRUGUZTIMJQGY__;!!PvXuogZ4sRB2p-tU!FrZjeE76JdRvt7hAVFgWspBl1k0aD06sNdYqA1GdoFWKK20LhMjw7ZzG1QGpaHuHaJKtvpzfOyyTVj11FLXW4g$>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[yinlabniu]

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

________________________________ 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) Caution: Non-NU Email 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 — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/linnabrown/run_dbcan/issues/160*issuecomment-1924534106__;Iw!!PvXuogZ4sRB2p-tU!FrZjeE76JdRvt7hAVFgWspBl1k0aD06sNdYqA1GdoFWKK20LhMjw7ZzG1QGpaHuHaJKtvpzfOyyTVj1jej2_4Q$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEXNKZQIG3Q6MIZCSITKJFTYRU4I3AVCNFSM6AAAAABCPM5GFGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMRUGUZTIMJQGY__;!!PvXuogZ4sRB2p-tU!FrZjeE76JdRvt7hAVFgWspBl1k0aD06sNdYqA1GdoFWKK20LhMjw7ZzG1QGpaHuHaJKtvpzfOyyTVj11FLXW4g$>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[linnabrown]

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]

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]

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]

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