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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
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MERGE: 6.2.0 Integrated Pipelines #274

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago

Starting to track pre-merge.

There seems to be a problem with VF graphs not being sent (or retrievable??) from phylotyper. It should be on the VF graph generation end as phylotyper hasnt really changed.

kevinkle commented 6 years ago 

modules.phylotyper.phylotyper.phylotyper(None, 'eae', '/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_pteae.tsv', id_file='/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_id.txt') from multiplesa08a361e-0656-4c95-b474-d02f521fe5c5Failed 5 minutes agoTraceback (most recent call last):   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job     rv = job.perform()   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform     self._result = self.func(*self.args, **self.kwargs)   File "./modules/phylotyper/phylotyper.py", line 94, in phylotyper     subtype Exception: phylotyper.phylotyper() could not retrieve reference sequences for loci: [rdflib.term.URIRef(u'https://www.github.com/superphy#eae')], uriIsolate: https://www.github.com/superphy#spfy6, subtype: eae | 6 minutes ago | Requeue Cancel
-- | -- | --
modules.phylotyper.phylotyper.to_dict('/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx1.tsv', 'stx1', '/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx1.p') from multiples94b59eac-589d-4046-b459-2017f40d1ac6Failed 5 minutes agoTraceback (most recent call last):   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job     rv = job.perform()   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform     self._result = self.func(*self.args, **self.kwargs)   File "./modules/phylotyper/phylotyper.py", line 122, in to_dict     str(pt_results) Exception: phylotyper.to_dict() couldnt find loci for file: /datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx1.tsv, subtype: stx1, pickle_file, /datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx1.p, with dataframe Empty DataFrame Columns: [genome, tree_label, subtype, probability, phylotyper_assignment, loci] Index: [] | 6 minutes ago | Requeue Cancel
modules.phylotyper.phylotyper.to_dict('/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx2.tsv', 'stx2', '/datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx2.p') from multiples43666c1d-32cf-4625-b3de-698f984b3aa9Failed 5 minutes agoTraceback (most recent call last):   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job     rv = job.perform()   File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform     self._result = self.func(*self.args, **self.kwargs)   File "./modules/phylotyper/phylotyper.py", line 122, in to_dict     str(pt_results) Exception: phylotyper.to_dict() couldnt find loci for file: /datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx2.tsv, subtype: stx2, pickle_file, /datastore/2018-03-11-03-35-02-656350-ECI-2644_lcl.fasta_ptstx2.p, with dataframe Empty DataFrame Columns: [genome, tree_label, subtype, probability, phylotyper_assignment, loci] Index: [] | 6 minutes ago | Requeue Cancel

eae isn't retrieved in markerseqs = MarkerSequences(loci), but stx1 and stx2 is going through to to_dict().

kevinkle commented 6 years ago

I'm not seeing any changes that would cause this issue. Going to try and revert the Blazegraph ver in case inferencing got turned off. EDIT: nvm, master was on old image anyways.

kevinkle commented 6 years ago

This is new, after changing all eaeH/eae... to eae.

 modules.phylotyper.phylotyper.to_dict('/datastore/2018-03-11-04-16-38-210778-ECI-2644_lcl.fasta_pteae.tsv', 'eae', '/datastore/2018-03-11-04-16-38-210778-ECI-2644_lcl.fasta_pteae.p') from multiples
92fae15a-2353-4a0a-996d-555b51230b14
Failed 1 minute ago
Traceback (most recent call last):
  File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/worker.py", line 700, in perform_job
    rv = job.perform()
  File "/opt/conda/envs/backend/lib/python2.7/site-packages/rq/job.py", line 500, in perform
    self._result = self.func(*self.args, **self.kwargs)
  File "./modules/phylotyper/phylotyper.py", line 122, in to_dict
    str(pt_results)
Exception: phylotyper.to_dict() couldnt find loci for file: /datastore/2018-03-11-04-16-38-210778-ECI-2644_lcl.fasta_pteae.tsv, subtype: eae, pickle_file, /datastore/2018-03-11-04-16-38-210778-ECI-2644_lcl.fasta_pteae.p, with dataframe        genome      tree_label         subtype     probability  \
0  lcl|query|  not applicable  not applicable  not applicable   

              phylotyper_assignment            loci  
0  Subtype loci not found in genome  not applicable
kevinkle commented 6 years ago

Merging.

CHANGELOG:

TODO: