Receiving a "No descriptions found for your id's" for GT2

[carleton-envbiotech]

Hello,

I've recently been running DRAM v1.4.6 that was installed manually on a Linux server. It is running smoothly and outputting the desired files, but I am getting a warning I have never seen (see below):

/datastore/tools/lib/python3.9/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(...)

It looks like it is having issue with a lone CAZyme category, but I am getting hits for GT2 gene id in the metabolism_summary Excel file. Is this an issue with my database descriptions that I could resolve? Note, I am not running DRAM in a conda environment in this case.

[yyyuechen]

Hi, I got the same warning with running DRAM v1.5.0, did you figure it out what could be the solution?

[carleton-envbiotech]

I have not managed to solve it yet, although this may be related to having DRAM natively installed and/or a database issue. I am going to try and do everything through mamba and update all the databases and try again.

[yyyuechen]

I run my command on a remote platform so it shouldn't be the database/installation issue, but now I don't have this error anymore after I made more space to store the intermediate files, and before I run my dram command I have extra commands like this:

module purge
export PERL5LIB=
module load dram/1.5.0

hope this can help, good luck :D!

[carleton-envbiotech]

@yyyuechen any idea how you would apply this to using it with conda? The commands aren't working for me and I am getting the same error message after a fresh install of DRAM 1.5.0

[carleton-envbiotech]

I tried this again for the same genome using V11 (default installed by DRAM) and V12 (most up to date version available from dbCAN) to annotate a single genome with the accession number GCA_009877435.1_ASM987743v1 and received different warnings related to dbCAN/CAZymes:

#V12 message

/datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GH179 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GH179 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_3 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_trans_2_3 look like an id from dbcan_description warnings.warn(

#V11 message

2024-03-03 20:27:51,516 - Annotating GCA_009877435.1_ASM987743v1_genomic 2024-03-03 20:28:42,742 - Turning genes from prodigal to mmseqs2 db 2024-03-03 20:28:44,401 - Getting hits from kofam 2024-03-03 20:44:46,953 - One of your requested annotation databases is missing. If you did not specify KEGG database, distillate will be of limited use. If no CAMPER source was provided (as of DRAM v1.5.0, it is still not automatically included), and you want to annotate with CAMPER - see instructions on GitHub for downloading if you would like to run this tool as a standalone: https://github.com/WrightonLabCSU/CAMPER. 2024-03-03 20:44:46,954 - Getting forward best hits from peptidase 2024-03-03 20:44:52,508 - Getting reverse best hits from peptidase 2024-03-03 20:44:53,813 - Getting descriptions of hits from peptidase 2024-03-03 20:44:54,170 - Getting hits from pfam 2024-03-03 20:45:03,891 - Getting hits from dbCAN /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_3 look like an id from dbcan_description warnings.warn( 2024-03-03 20:45:18,994 - Merging ORF annotations 2024-03-03 20:45:39,840 - No rRNAs were detected, no rrnas.tsv file will be created.

So it seems that even updating to V12 of dbCAN doesn't fix the issue, but rather introduces further warnings. Is there an issue with updating the description db in DRAM to address this? I've tried updating the description forms and distillation forms as well, but my understanding is updating the description form is only to update DRAM when new databases have been brought in and it's more for setting locations.

[yyyuechen]

I tried this again for the same genome using V11 (default installed by DRAM) and V12 (most up to date version available from dbCAN) to annotate a single genome with the accession number GCA_009877435.1_ASM987743v1 and received different warnings related to dbCAN/CAZymes:

#V12 message

/datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GH179 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GH179 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_3 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda_dbCAN_updated/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_trans_2_3 look like an id from dbcan_description warnings.warn(

#V11 message

2024-03-03 20:27:51,516 - Annotating GCA_009877435.1_ASM987743v1_genomic 2024-03-03 20:28:42,742 - Turning genes from prodigal to mmseqs2 db 2024-03-03 20:28:44,401 - Getting hits from kofam 2024-03-03 20:44:46,953 - One of your requested annotation databases is missing. If you did not specify KEGG database, distillate will be of limited use. If no CAMPER source was provided (as of DRAM v1.5.0, it is still not automatically included), and you want to annotate with CAMPER - see instructions on GitHub for downloading if you would like to run this tool as a standalone: https://github.com/WrightonLabCSU/CAMPER. 2024-03-03 20:44:46,954 - Getting forward best hits from peptidase 2024-03-03 20:44:52,508 - Getting reverse best hits from peptidase 2024-03-03 20:44:53,813 - Getting descriptions of hits from peptidase 2024-03-03 20:44:54,170 - Getting hits from pfam 2024-03-03 20:45:03,891 - Getting hits from dbCAN /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glycos_transf_2 look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description warnings.warn( /datastore/tools/gregoire/envs/DRAM_conda/lib/python3.10/site-packages/mag_annotator/database_handler.py:218: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_3 look like an id from dbcan_description warnings.warn( 2024-03-03 20:45:18,994 - Merging ORF annotations 2024-03-03 20:45:39,840 - No rRNAs were detected, no rrnas.tsv file will be created.

So it seems that even updating to V12 of dbCAN doesn't fix the issue, but rather introduces further warnings. Is there an issue with updating the description db in DRAM to address this? I've tried updating the description forms and distillation forms as well, but my understanding is updating the description form is only to update DRAM when new databases have been brought in and it's more for setting locations.

did you check that if you have enough space? because dram can generate a very big intermediate file during its run, I am not sure if this is the case, try to run one file with dram to see if your script work. also I don't have experience running dram on conda, maybe try this (I am not sure if this can help, but it works for me when I have a problem in installing an environment via conda):
alias | grep python #check if there is python aliation
unalias python
nano ~/.bashrc #if alias, remove the line
python3 -m pip install pip --upgrade
pip install pyopenssl --upgrade