I ran DRAM for 9 MAGs and it gave me an error that the object has no attribute query, can you please go through the log file and try to resolve this error so that I can complete the analysis successfully. One thing I would like you to know is that while setting up the databases, it gave an error for the VOG database, but since it has processed databases for the uniref, kofam and dBcan so I thought it would not be a problem to run the annotation for the MAGs. So, do you think that could the issue? I am posting the screenshot of the terminal output for the database setting up command where it gave the error.
2023-05-30 13:10:06,820 - The log file is created at /home/saraswati/DRAM_TRIAL_ANNOTATION/ANNOTATION/annotate.log.
2023-05-30 13:10:06,820 - 9 FASTAs found
/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None
warnings.warn("Database does not exist at path %s" % description_loc)
2023-05-30 13:10:06,871 - Starting the Annotation of Bins 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: 05/22/2023, 13:45:41
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: 05/22/2023, 13:45:47
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: 05/27/2023, 02:10:54
Origin: Downloaded by DRAM
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: 05/27/2023, 02:13:56
Origin: Downloaded by DRAM
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: 05/27/2023, 02:10:57
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: 05/27/2023, 02:14:02
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: 05/27/2023, 02:14:05
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: 05/27/2023, 02:23:06
Origin: Downloaded by DRAM
2023-05-30 13:10:06,873 - Retrieved database locations and descriptions
2023-05-30 13:10:06,874 - Annotating A5_bin.15
2023-05-30 13:10:20,059 - Turning genes from prodigal to mmseqs2 db
2023-05-30 13:10:30,512 - Getting hits from kofam
2023-05-30 13:22:12,768 - Getting hits from pfam
Traceback (most recent call last):
File "/home/saraswati/conda/anaconda3/envs/dram/bin/DRAM.py", line 207, in
args.func(**args_dict)
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1513, in annotate_bins
all_annotations = annotate_fastas(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1394, in annotate_fastas
annotate_fasta(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1239, in annotate_fasta
annotations = annotate_orfs(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1091, in annotate_orfs
run_mmseqs_profile_search(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 256, in run_mmseqs_profile_search
pfam_descriptions = db_handler.get_descriptions(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 205, in get_descriptions
descriptions = [
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 208, in
for des in self.session.query(description_class)
AttributeError: 'NoneType' object has no attribute 'query'
Does any of this ring any bells? Kindly help me resolve the error.
Thanks in Advance
Saras :)
Hi @rmFlynn @ileleiwi @rdenise
I ran DRAM for 9 MAGs and it gave me an error that the object has no attribute query, can you please go through the log file and try to resolve this error so that I can complete the analysis successfully. One thing I would like you to know is that while setting up the databases, it gave an error for the VOG database, but since it has processed databases for the uniref, kofam and dBcan so I thought it would not be a problem to run the annotation for the MAGs. So, do you think that could the issue? I am posting the screenshot of the terminal output for the database setting up command where it gave the error.
2023-05-30 13:10:06,820 - The log file is created at /home/saraswati/DRAM_TRIAL_ANNOTATION/ANNOTATION/annotate.log. 2023-05-30 13:10:06,820 - 9 FASTAs found /home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at path %s" % description_loc) 2023-05-30 13:10:06,871 - Starting the Annotation of Bins 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: 05/22/2023, 13:45:41 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: 05/22/2023, 13:45:47 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: 05/27/2023, 02:10:54 Origin: Downloaded by DRAM 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: 05/27/2023, 02:13:56 Origin: Downloaded by DRAM
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: 05/27/2023, 02:10:57 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: 05/27/2023, 02:14:02 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: 05/27/2023, 02:14:05 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: 05/27/2023, 02:23:06 Origin: Downloaded by DRAM
2023-05-30 13:10:06,873 - Retrieved database locations and descriptions 2023-05-30 13:10:06,874 - Annotating A5_bin.15 2023-05-30 13:10:20,059 - Turning genes from prodigal to mmseqs2 db 2023-05-30 13:10:30,512 - Getting hits from kofam 2023-05-30 13:22:12,768 - Getting hits from pfam Traceback (most recent call last): File "/home/saraswati/conda/anaconda3/envs/dram/bin/DRAM.py", line 207, in
args.func(**args_dict)
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1513, in annotate_bins
all_annotations = annotate_fastas(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1394, in annotate_fastas
annotate_fasta(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1239, in annotate_fasta
annotations = annotate_orfs(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 1091, in annotate_orfs
run_mmseqs_profile_search(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/annotate_bins.py", line 256, in run_mmseqs_profile_search
pfam_descriptions = db_handler.get_descriptions(
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 205, in get_descriptions
descriptions = [
File "/home/saraswati/conda/anaconda3/envs/dram/lib/python3.9/site-packages/mag_annotator/database_handler.py", line 208, in
for des in self.session.query(description_class)
AttributeError: 'NoneType' object has no attribute 'query'
Does any of this ring any bells? Kindly help me resolve the error. Thanks in Advance Saras :)