dbCAN

[JoseLopezArcondo]

Hello, I could set up DRAM and I am running it without KEGG database. I found this warning happening every time. Is there anything going wrong here or just a problem happening with this very specific function? 2023-02-04 22:04:16,528 - Getting hits from dbCAN /home/jose/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn(

I Also added the --threads 20 tag, but doesn't seem to be using them according to the CPU load I see

Thanks a lot

[dmitrisvetlov]

Hello @JoseLopezArcondo,

Can you please give us more details about what you are trying to do? For example, please post the specific command you are using to run DRAM, with all arguments?

Thanks, Dmitri Svetlov

[Somebodyatthdoor]

Hi, I am also having exactly the same error, it occurs for pretty much every one of my MAGs. It seems to only be happening for SLH and versions of GT2:

• database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description
• • database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description
• database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_3 look like an id from dbcan_description

The command I am running is: DRAM.py annotate -i "./drep/dereplicated_genomes/*.fa" -o dram_output_95 --threads 8

I'm using the newest version of DRAM (DRAM_v1.4.6), and I prepared the DRAM database using: DRAM-setup.py prepare_databases --output_dir DRAM_data --kegg_loc ./data/kegg_data/genus_prokaryotes.pep

Cheers, Laura

[Somebodyatthdoor]

Hi,

Just to update. I have recently tried rerunning this with the newest version of DRAM and I am still encountering this specific error. Still just for SLH and GT2_Glycos_transf_2.

The program still runs to completion despite the error. In your opinion, is this an error that can be ignored: ie. it won't affect the analysis?

Cheers, Laura

[BurchamLab]

Has anyone fixed this issue? I am also getting "UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn("

It seems to only impact cazy annotation though

[BurchamLab]

Hi Laura, did you ever get this fixed?

[Somebodyatthdoor]

Hi @zburcham

No unfortunately not. I am currently trying several different things to see if they fix it, but it takes so long to make databases that troubleshooting anything takes a long time.

When you go on to run distill with your annotation files where this error has occurred, do you also have issues with the output from that? Originally I thought the dbcan issue may not be too much of a problem, but when I run distill on the annotation output files I get practically zero hits for anything, I'm currently trying to work out if these are two separate problems or if they are both caused by the same issue.

Cheers, Laura

[BurchamLab]

Hi @Somebodyatthdoor , the warning shows up for me during the annotate step. Distill looks to work fine outside of cazy. I also have a lot of zeros but I do have expected hits which makes me think it is just cazy.

[Somebodyatthdoor]

Hi @zburcham. I used to get far more hits from distill prior to this issue, which is what made me think they might be linked. But if it is working fine for you then I guess they are unlinked problems.

[Somebodyatthdoor]

Hi @zburcham, did you find a solution to this in the end? I am still having the same issue, not sure if it will impact the distill results.

[BurchamLab]

@Somebodyatthdoor, unfortunately I never got improved dbCan results but the other databases worked fine.

All the best,

Zachary M. Burcham, PhD Research Assistant Professor Department of Microbiology University of Tennessee-Knoxville

On Oct 19, 2023, at 4:03 AM, Somebodyatthdoor @.***> wrote:

Hi @zburcham https://github.com/zburcham, did you find a solution to this in the end? I am still having the same issue, not sure if it will impact the distill results.

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