problem about dramv-annotate

[xjhzjucas]

Hi developer, I met a lot of warmings when running dramv-annotate: it looks like:

2024-03-07 09:45:29,681 - 1 fastas found
2024-03-07 09:45:29,681 - Checking for duplicate names
2024-03-07 09:45:29,817 - No duplicate names found
2024-03-07 09:45:29,817 - Starting the Viral Annotation of Genes with database configuration:


KOfam db:
    Citation: T. Aramaki, R. Blanc-Mathieu, H. Endo, K. Ohkubo, M. Kanehisa, S. Goto, and H. Ogata, "Kofamkoala: Kegg ortholog assignment based on profile hmm and adaptive score threshold," Bioinformatics, vol. 36, no. 7, pp. 2251–2252, 2020.
    Download Time: 01/20/2024, 16:25:42
    Origin: Downloaded by DRAM
KOfam KO list:
    Citation: T. Aramaki, R. Blanc-Mathieu, H. Endo, K. Ohkubo, M. Kanehisa, S. Goto, and H. Ogata, "Kofamkoala: Kegg ortholog assignment based on profile hmm and adaptive score threshold," Bioinformatics, vol. 36, no. 7, pp. 2251–2252, 2020.
    Download Time: 01/20/2024, 16:25:44
    Origin: Downloaded by DRAM
Pfam db:
    Citation: J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G. A. Salazar, E. L. Sonnhammer, S. C. Tosatto, L. Paladin, S. Raj, L. J. Richardson et al., "Pfam: The protein families database in 2021," Nucleic acids research, vol. 49, no. D1, pp. D412–D419, 2021.
    Download Time: 01/20/2024, 17:34:00
    Origin: Downloaded by DRAM
    Description_Db_Updated: 01/20/2024, 18:29:04
dbCAN db:
    Citation: Y. Yin, X. Mao, J. Yang, X. Chen, F. Mao, and Y. Xu, "dbcan: a web resource for automated carbohydrate-active enzyme annotation," Nucleic acids research, vol. 40, no. W1, pp. W445–W451, 2012.
    Version: 11
    Download Time: 01/20/2024, 17:34:28
    Origin: Downloaded by DRAM
    Description_Db_Updated: 01/20/2024, 18:29:04
RefSeq Viral db:
    Description_Db_Updated: 01/20/2024, 18:28:34
    Citation: J. R. Brister, D. Ako-Adjei, Y. Bao, and O. Blinkova, "Ncbi viral genomes resource," Nucleic acids research, vol. 43, no. D1, pp. D571–D577, 2015. [3] M. Kanehisa, M. Furumichi, Y. Sato, M. Ishiguro-Watanabe, and M. Tan-abe, "Kegg: integrating viruses and cellular organisms," Nucleic acids research, vol. 49, no. D1, pp. D545–D551, 2021.
    Viral_Files: 1
    Download Time: 01/20/2024, 17:37:02
    Origin: Downloaded by DRAM
MEROPS peptidase db:
    Description_Db_Updated: 01/20/2024, 18:29:03
    Citation: N. D. Rawlings, A. J. Barrett, P. D. Thomas, X. Huang, A. Bateman, and R. D. Finn, "The merops database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the panther database," Nucleic acids research, vol. 46, no. D1, pp. D624–D632, 2018.
    Download Time: 01/20/2024, 17:38:49
    Origin: Downloaded by DRAM
VOGDB db:
    Citation: J. Thannesberger, H.-J. Hellinger, I. Klymiuk, M.-T. Kastner, F. J. Rieder, M. Schneider, S. Fister, T. Lion, K. Kosulin, J. Laengle et al., "Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples," The FASEB Journal, vol. 31, no. 5, pp. 1987–2000, 2017.
    Version: latest
    Download Time: 01/20/2024, 17:36:24
    Origin: Downloaded by DRAM
    Description_Db_Updated: 01/20/2024, 18:29:06

Pfam hmm dat:
    Description_Db_Updated: Unknown, or Never
    Citation: J. Mistry, S. Chuguransky, L. Williams, M. Qureshi, G. A. Salazar, E. L. Sonnhammer, S. C. Tosatto, L. Paladin, S. Raj, L. J. Richardson et al., "Pfam: The protein families database in 2021," Nucleic acids research, vol. 49, no. D1, pp. D412–D419, 2021.
    Download Time: 01/20/2024, 17:34:03
    Origin: Downloaded by DRAM
dbCAN family activities:
    Citation: Y. Yin, X. Mao, J. Yang, X. Chen, F. Mao, and Y. Xu, "dbcan: a web resource for automated carbohydrate-active enzyme annotation," Nucleic acids research, vol. 40, no. W1, pp. W445–W451, 2012.
    Version: 11
    Upload_Date: 08062022
    Download Time: 01/20/2024, 17:34:29
    Origin: Downloaded by DRAM
dbCAN subfamily EC numbers:
    Citation: Y. Yin, X. Mao, J. Yang, X. Chen, F. Mao, and Y. Xu, "dbcan: a web resource for automated carbohydrate-active enzyme annotation," Nucleic acids research, vol. 40, no. W1, pp. W445–W451, 2012.
    Version: 11
    Upload_Date: 08062022
    Download Time: 01/20/2024, 17:34:31
    Origin: Downloaded by DRAM
VOG annotations:
    Description_Db_Updated: Unknown, or Never
    Citation: J. Thannesberger, H.-J. Hellinger, I. Klymiuk, M.-T. Kastner, F. J. Rieder, M. Schneider, S. Fister, T. Lion, K. Kosulin, J. Laengle et al., "Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples," The FASEB Journal, vol. 31, no. 5, pp. 1987–2000, 2017.
    Version: latest
    Download Time: 01/20/2024, 17:36:26
    Origin: Downloaded by DRAM

Genome summary form:
    Branch: master
    Download Time: 01/20/2024, 17:38:50
    Origin: Downloaded by DRAM
Module step form:
    Branch: master
    Download Time: 01/20/2024, 17:38:52
    Origin: Downloaded by DRAM
ETC module database:
    Branch: master
    Download Time: 01/20/2024, 17:38:54
    Origin: Downloaded by DRAM
Function heatmap form:
    Branch: master
    Download Time: 01/20/2024, 17:38:52
    Origin: Downloaded by DRAM
AMG database:
    Branch: master
    Download Time: 01/20/2024, 17:38:53
    Origin: Downloaded by DRAM
2024-03-07 09:45:29,817 - Retrieved database locations and descriptions
2024-03-07 09:45:29,817 - Annotating final-viral-combined-for-dramv
2024-03-07 09:59:06,735 - Turning genes from prodigal to mmseqs2 db
2024-03-07 09:59:10,487 - Getting hits from kofam
2024-03-07 13:52:00,018 - Getting forward best hits from viral
2024-03-07 13:55:15,036 - Getting reverse best hits from viral
2024-03-07 13:55:41,549 - Getting descriptions of hits from viral
2024-03-07 13:55:47,910 - Getting forward best hits from peptidase
2024-03-07 13:57:59,111 - Getting reverse best hits from peptidase
2024-03-07 13:58:02,338 - Getting descriptions of hits from peptidase
2024-03-07 13:58:06,975 - Getting hits from pfam
2024-03-07 13:58:57,429 - Getting hits from dbCAN
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description
  warnings.warn(
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/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(
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_5 look like an id from dbcan_description
  warnings.warn(
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this GT2_Glyco_tranf_2_4 look like an id from dbcan_description
  warnings.warn(
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/database_handler.py:215: UserWarning: No descriptions were found for your id's. Does this SLH look like an id from dbcan_description
  warnings.warn(
2024-03-07 14:04:40,247 - Getting hits from VOGDB
2024-03-07 19:08:01,265 - Merging ORF annotations
2024-03-07 22:33:43,311 - Annotations complete, processing annotations
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py:189: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
  virsorter_genes['start_position'] = virsorter_genes['start_position'].astype(int)
/mnt/sdb/xjh/miniconda3/envs/suv_threesoft/lib/python3.10/site-packages/mag_annotator/annotate_vgfs.py:190: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame.
Try using .loc[row_indexer,col_indexer] = value instead

I don't know will this infect the results? How can I solve this? Thank you!

[pengzhuobing]

Have you solved this?

[sahilrishav2]

@pengzhuobing , @xjhzjucas . Has any one of you able to understand the issue ? I am also getting the same issue.

[BioRRW]

Thank you for choosing to use DRAM. Unfortunately, at this time, we do not have the capacity to provide support for DRAM. We appreciate your understanding and encourage you to stay tuned for the release of DRAM2, expected in 2025.

Best regards, DRAM dev team