Comments (4)
laurensvdwiel
commented on July 4, 2024
Hi Coos, the pull request contains all changes needed for this issue to be recolved. Please check it out and close if resolved
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laurensvdwiel
commented on July 4, 2024
Fixed per #21
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cbaakman
commented on July 4, 2024
The problem doesn't seem to be completely fixed. I've pulled from the master branch, rebuilt with docker-compose, but the message keeps showing:
ERROR:PF01391: Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 382, in trace_task
R = retval = fun(*args, **kwargs)
File "/usr/src/app/metadome/factory.py", line 90, in __call__
return TaskBase.__call__(self, *args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 641, in __protected_call__
return self.run(*args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/base.py", line 467, in run
return task._orig_run(*args, **kwargs)
File "/usr/src/app/metadome/tasks.py", line 73, in initialize_metadomain
return MetaDomain.initializeFromDomainID(domain_id)
File "/usr/src/app/metadome/domain/models/entities/meta_domain.py", line 138, in initializeFromDomainID
meta_codons_per_consensus_pos, consensus_length, n_instances = generate_pfam_aligned_codons(domain_id)
File "/usr/src/app/metadome/domain/data_generation/mapping/meta_domain_mapping.py", line 133, in generate_pfam_aligned_codons
raise Exception("duplicate uniprot position in metadomain for uniprot_ac ='"+str(_alignment['uniprot_ac'])+"' at position '"+str(uniprot_pos)+"'")
Exception: duplicate uniprot position in metadomain for uniprot_ac ='Q9Y215-5' at position '200'
INFO:PF01393: <MetaDomain(domain_id='PF01393', consensus_length='53', n_proteins='3', n_instances='3')>
INFO:PF00999: <MetaDomain(domain_id='PF00999', consensus_length='381', n_proteins='23', n_instances='23')>
INFO:PF04117: <MetaDomain(domain_id='PF04117', consensus_length='62', n_proteins='4', n_instances='4')>
INFO:PF00052: <MetaDomain(domain_id='PF00052', consensus_length='132', n_proteins='10', n_instances='14')>
INFO:PF00157: <MetaDomain(domain_id='PF00157', consensus_length='72', n_proteins='26', n_instances='27')>
INFO:PF03950: <MetaDomain(domain_id='PF03950', consensus_length='174', n_proteins='3', n_instances='3')>
INFO:PF00206: <MetaDomain(domain_id='PF00206', consensus_length='312', n_proteins='6', n_instances='7')>
INFO:PF00447: <MetaDomain(domain_id='PF00447', consensus_length='96', n_proteins='7', n_instances='7')>
INFO:PF03662: <MetaDomain(domain_id='PF03662', consensus_length='318', n_proteins='7', n_instances='7')>
INFO:PF01795: <MetaDomain(domain_id='PF01795', consensus_length='309', n_proteins='3', n_instances='3')>
ERROR:PF02389: Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 382, in trace_task
R = retval = fun(*args, **kwargs)
File "/usr/src/app/metadome/factory.py", line 90, in __call__
return TaskBase.__call__(self, *args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 641, in __protected_call__
return self.run(*args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/base.py", line 467, in run
return task._orig_run(*args, **kwargs)
File "/usr/src/app/metadome/tasks.py", line 73, in initialize_metadomain
return MetaDomain.initializeFromDomainID(domain_id)
File "/usr/src/app/metadome/domain/models/entities/meta_domain.py", line 138, in initializeFromDomainID
meta_codons_per_consensus_pos, consensus_length, n_instances = generate_pfam_aligned_codons(domain_id)
File "/usr/src/app/metadome/domain/data_generation/mapping/meta_domain_mapping.py", line 133, in generate_pfam_aligned_codons
raise Exception("duplicate uniprot position in metadomain for uniprot_ac ='"+str(_alignment['uniprot_ac'])+"' at position '"+str(uniprot_pos)+"'")
Exception: duplicate uniprot position in metadomain for uniprot_ac ='Q9UBC9' at position '66'
INFO:PF02366: <MetaDomain(domain_id='PF02366', consensus_length='245', n_proteins='5', n_instances='5')>
INFO:PF02044: <MetaDomain(domain_id='PF02044', consensus_length='14', n_proteins='5', n_instances='5')>
INFO:PF00538: <MetaDomain(domain_id='PF00538', consensus_length='74', n_proteins='14', n_instances='18')>
INFO:PF01088: <MetaDomain(domain_id='PF01088', consensus_length='211', n_proteins='7', n_instances='7')>
INFO:PF00618: <MetaDomain(domain_id='PF00618', consensus_length='105', n_proteins='46', n_instances='46')>
ERROR:PF00038: Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 382, in trace_task
R = retval = fun(*args, **kwargs)
File "/usr/src/app/metadome/factory.py", line 90, in __call__
return TaskBase.__call__(self, *args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 641, in __protected_call__
return self.run(*args, **kwargs)
File "/usr/local/lib/python3.5/site-packages/celery/app/base.py", line 467, in run
return task._orig_run(*args, **kwargs)
File "/usr/src/app/metadome/tasks.py", line 73, in initialize_metadomain
return MetaDomain.initializeFromDomainID(domain_id)
File "/usr/src/app/metadome/domain/models/entities/meta_domain.py", line 138, in initializeFromDomainID
meta_codons_per_consensus_pos, consensus_length, n_instances = generate_pfam_aligned_codons(domain_id)
File "/usr/src/app/metadome/domain/data_generation/mapping/meta_domain_mapping.py", line 133, in generate_pfam_aligned_codons
raise Exception("duplicate uniprot position in metadomain for uniprot_ac ='"+str(_alignment['uniprot_ac'])+"' at position '"+str(uniprot_pos)+"'")
Exception: duplicate uniprot position in metadomain for uniprot_ac ='Q14CN4-3' at position '320'
@laurensvdwiel could you test for these specific accession codes?
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laurensvdwiel
commented on July 4, 2024
Stupid me forgot to include a commit in the pull request, added this now
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Related Issues (20)
- Visualization idea: Add options for color selection, to allow users to select a color for marking positions
- In the domain overlay, sometimes the number of aligned homologues is undefined HOT 1
- Add ESC as a manner to escape the positional and domain overview overlays HOT 1
- Unsupported browser warning is also shown for newer chrome versions
- Visualization suggestion: different colours for selecting and annotation of ClinVar variants
- Visualization suggestion: Different colours for ClinVar within gene and from Homologue
- Improve gunicorn in docker images HOT 3
- Information improvement: Add number of missense/synonymous information to raw data output
- Downloadable resource HOT 10
- Some genes don't have any transcripts available for selection
- Provide access to the visualization of an ENST* via the dashboard link HOT 1
- Error since newest release: DisabledBackend Attribute error HOT 4
- Additional information: Annotate/Visualize exon regions
- Visualization suggestion: Add amino acid preferences as a heatmap to the meta-domain landscape
- Add hg38 support HOT 1
- Add gene symbol entry for dashboard
- Is project alive? HOT 2
- Change support request subject to a preset in default_settings
- Add reCAPTCHA-like functionality to contact form
- could not connect to server: No route to host HOT 1
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