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Homology Modeling Service

Python 91.71% Shell 0.91% JavaScript 1.19% CSS 0.26% HTML 5.94%

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jonblack cbaakman rnaimehaom

hommod's Issues

Add update mechanism

The update scripts produce models before they are needed so future requests are quick. When a model doesn't exist, it's produced on-the-fly which is time consuming.

The update script was being run on bamboo but the produced files were never used by the frontend on chelonium. The service has since been removed from bamboo because it makes more sense to run the script on chelonium.

The docker scripts need updating to add the updating as a separate process. Care needs to be taken to ensure it doesn't slow the machine down too much.

TYPE is now 8-bit binary

HOPE gets the following error from HOMMOD:

Exception: the following models have failed:
f1a9c8ce-7bb9-feda-7ad6-f527c0b3de8f_HUMAN_175-298_3NOG-D:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 967, in modelProc
    main_domain_alignment, main_domain_range)
  File "/usr/src/app/hommod_rest/services/model.py", line 465, in _collect_template
    raise e
IOError: [Errno ftp error] 200 TYPE is now 8-bit binary

What is the cause?

UnboundLocalError: local variable 'lockfile_path' referenced before assignment

I get the following error in HOPE from hommod:

        Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hope/factory.py", line 171, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hope/tasks.py", line 206, in get_structure_features
    model = modeler.from_sequence(sequence, position, template_id)
  File "/usr/src/app/hope/domain/modeler.py", line 14, in from_sequence
    template_id)
  File "/usr/src/app/hope/services/hommod.py", line 68, in run
    raise ServiceError(json.loads(r.text)['message'])
hope.services.types.ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 35, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 1003, in modelProc
    _log.debug("ending lock on {}".format(lockfile_path))
UnboundLocalError: local variable 'lockfile_path' referenced before assignment

get_metadata endpoint returns an empty string

The get_metadata endpoint has two related issues:

It always returns an empty string
The empty string isn't in JSON format

job queue returns wrong status

When a job is started using the frontend's submit method, followed by a call to the status method (see: https://github.com/cmbi/hommod-rest/blob/master/hommod_rest/frontend/api/endpoints.py#L38), it does not always return the right status. Status STARTED has been observed for jobs that had already finished or failed.

mistake

Inefficient functions

There are a few functions that have O(n^3) or worse running time (based on a quick analysis, it's actually more complex than that). In any case, these functions have 4-6 nested loops.

TypeError: 'dict' object is not callable

HOPE is getting a lot of internal server errors from hommod. In the logs I see:

[2016-03-02 08:26:38 +0000] [2167] [ERROR] Error handling request
Traceback (most recent call last):
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/gunicorn/workers/async.py", line 52, in handle
    self.handle_request(listener_name, req, client, addr)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/gunicorn/workers/ggevent.py", line 159, in handle_request
    super(GeventWorker, self).handle_request(*args)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/gunicorn/workers/async.py", line 105, in handle_request
    respiter = self.wsgi(environ, resp.start_response)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1836, in __call__
    return self.wsgi_app(environ, start_response)
  File "/srv/www/hommod/hommod-rest/hommod_rest/middleware.py", line 44, in __call__
    return self.app(environ, start_response)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1820, in wsgi_app
    response = self.make_response(self.handle_exception(e))
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1403, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
    response = self.full_dispatch_request()
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1478, in full_dispatch_request
    response = self.make_response(rv)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/flask/app.py", line 1577, in make_response
    rv = self.response_class.force_type(rv, request.environ)
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/werkzeug/wrappers.py", line 841, in force_type
    response = BaseResponse(*_run_wsgi_app(response, environ))
  File "/srv/www/hommod/.virtualenvs/hommod-rest/local/lib/python2.7/site-packages/werkzeug/test.py", line 867, in run_wsgi_app
    app_rv = app(environ, start_response)
TypeError: 'dict' object is not callable

yasara deleting molecules on its own

For some models, yasara deletes molecules from the template while it's modeling. This leads to an error, because the number of molecules no longer matches the number of alignments.

Here's an example:

target sequence:

MGSKGVYQYHWQSHNVKHSGVDDMVLLSKITENSIVENLKKRYMDDYIFTYIGSVLISVNPFKQMPYFGEKEIEMYQGAAQYENPPHIYALADNMYRNMIIDRENQCVIISGESGAGKTVAAKYIMSYISRVSGGGTKVQHVKDIILQSNPLLEAFGNAKTVRNNNSSRFGKYFEIQFSPGGEPDGGKISNFLLEKSRVVMRNPGERSFHIFYQLIEGASAEQKHSLGITSMDYYYYLSLSGSYKVDDIDDRREFQETLHAMNVIGIFAEEQTLVLQIVAGILHLGNISFKEVGNYAAVESEEFLAFPAYLLGINQDRLKEKLTSRQMDSKWGGKSESIHVTLNVEQACYTRDALAKALHARVFDFLVDSINKAMEKDHEEYNIGVLDIYGFEIFQKNGFEQFCINFVNEKLQQIFIELTLKAEQEEYVQEGIRWTPIEYFNNKIVCDLIENKVNPPGIMSILDDVCATMHAVGEGADQTLLQKLQMQIGSHEHFNSWNQGFIIHHYAGKVSYDMDGFCERNRDVLFMDLIELMQSSELPFIKSLFPENLQADKKGRPTTAGSKIKKQANDLVSTLMKCTPHYIRCIKPNETKKPRDWEESRVKHQVEYLGLKENIRVRRAGYAYRRIFQKFLQRYAILTKATWPSWQGEEKQGVLHLLQSVNMDSDQFQLGRSKVFIKAPESLFLLEEMRERKYDGYARVIQKSWRKFVARKKYVQMREEASDLLLNKKERRRNSINRNFIGDYIGMEEHPELQQFVGKREKIDFADTVTKYDRRFKGVKRDLLLTPKCLYLIGREKVKQGPDKGLVKEVLKRKIEIERILSVSLSTMQDDIFILHEQEYDSLLESVFKTEFLSLLAKRYEEKTQKQLPLKFSNTLELKLKKENWGPWSAGGSRQVQFHQGFGDLAVLKPSNKVLQVSIGPGLPKNSRPTRRNTTQNTGYSSGTQNANYPVRAAPPPPGYHQNGVIRNQYVPYPHAPGSQRSNQKSLYTSMARPPLPRQQSTSSDRVSQTPESLDFLKVPDQGAAGVRRQTTSRPPPAGGRPKPQPKPKPQVPQCKALYAYDAQDTDELSFNANDIIDIIKEDPSGWWTGRLRGKQGLFPNNYVTKI

position: 346
species: HUMAN
template: 6C1D_P

interface not deleting mal-formed cookies

Whenever there's an error parsing the cookie, the badly-formed cookie simply stays and parsing keeps failing. Hommod should delete bad cookies and start with an empty object again.

HTTP Error 500: Internal Server Error

Message type: ERROR
Location: /usr/src/app/hope/services/hommod.py:68
Module: hommod
Function: run
Time: 2017-03-28 10:03:59,680
Message:
Model job failed:
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 60, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 786, in modelProc
    ranges = interpro.get_domain_locations(main_target_sequence)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 198, in get_domain_locations
    filepath = self._create_data_file(sequence)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 172, in _create_data_file
    status = _interpro_get_status(jobid)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 83, in _interpro_get_status
    return _interpro_get(_interpro_base_url + '/status/' + jobid)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 63, in _interpro_get
    reqH = urllib2.urlopen(req)
  File "/usr/local/lib/python2.7/urllib2.py", line 154, in urlopen
    return opener.open(url, data, timeout)
  File "/usr/local/lib/python2.7/urllib2.py", line 435, in open
    response = meth(req, response)
  File "/usr/local/lib/python2.7/urllib2.py", line 548, in http_response
    'http', request, response, code, msg, hdrs)
  File "/usr/local/lib/python2.7/urllib2.py", line 473, in error
    return self._call_chain(*args)
  File "/usr/local/lib/python2.7/urllib2.py", line 407, in _call_chain
    result = func(*args)
  File "/usr/local/lib/python2.7/urllib2.py", line 556, in http_error_default
    raise HTTPError(req.get_full_url(), code, msg, hdrs, fp)
HTTPError: HTTP Error 500: Internal Server Error

Yasara couldn't read PDB file

The following error happened via a call from HOPE:

  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 33, in create_model
    paths = modeler.modelProc (sequence, species_id, residue_number, False)
  File "/usr/src/app/hommod_rest/services/model.py", line 824, in modelProc
    domainalign.getAlignments (ranges, mainTargetSeq)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 709, in getAlignments
    if not secstr.hasSecStr(template):
  File "/usr/src/app/hommod_rest/services/secstr.py", line 62, in hasSecStr
    obj = self.yasara.LoadPDB (pdbfile)[0]
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 4773, in LoadPDB
    return(run(command[:-1]))
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 1012, in run
    if (command.find("\n")==-1): return(process("EXECUTE",command))
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 1006, in process
    result=com.receivemessage(com.RESULT)
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 812, in receivemessage
    raise RuntimeError("YASARA raised error %d: %s"%(messagedata[0],messagedata[1]))
RuntimeError: YASARA raised error 11: The file '/data/tmp/run-yasara-HUMAN-edadbbc0-7d72-e6ed-53f0-ad578d6b661e-51/3B8C.pdb' could not be read, make sure that the file is present and that you have read permissions.

HOPE's input sequence:

MGRGAGREYSPAATTAENGGGKKKQKEKELDELKKEVAMDDHKLSLDELGRKYQVDLSKGLTNQRAQDVLARDGPNALTPPPTTPEWVKFCRQLFGGFSILLWIGAILCFLAYGIQAAMEDEPSNDNLYLGVVLAAVVIVTGCFSYYQEAKSSKIMDSFKNMVPQQALVIREGEKMQINAEEVVVGDLVEVKGGDRVPADLRIISSHGCKVDNSSLTGESEPQTRSPEFTHENPLETRNICFFSTNCVEGTARGIVIATGDRTVMGRIATLASGLEVGRTPIAMEIEHFIQLITGVAVFLGVSFFVLSLILGYSWLEAVIFLIGIIVANVPEGLLATVTVCLTLTAKRMARKNCLVKNLEAVETLGSTSTICSDKTGTLTQNRMTVAHMWFDNQIHEADTTEDQSGATFDKRSPTWTALSRIAGLCNRAVFKAGQENISVSKRDTAGDASESALLKCIELSCGSVRKMRDRNPKVAEIPFNSTNKYQLSIHEREDSPQSHVLVMKGAPERILDRCSTILVQGKEIPLDKEMQDAFQNAYMELGGLGERVLGFCQLNLPSGKFPRGFKFDTDELNFPTEKLCFVGLMSMIDPPRAAVPDAVGKCRSAGIKVIMVTGDHPITAKAIAKGVGIISEGNETVEDIAARLNIPMSQVNPREAKACVVHGSDLKDMTSEQLDEILKNHTEIVFARTSPQQKLIIVEGCQRQGAIVAVTGDGVNDSPALKKADIGIAMGISGSDVSKQAADMILLDDNFASIVTGVEEGRLIFDNLKKSIAYTLTSNIPEITPFLLFIIANIPLPLGTVTILCIDLGTDMVPAISLAYEAAESDIMKRQPRNSQTDKLVNERLISMAYGQIGMIQALGGFFTYFVILAENGFLPSRLLGIRLDWDDRTMNDLEDSYGQEWTYEQRKVVEFTCHTAFFASIVVVQWADLIICKTRRNSVFQQGMKNKILIFGLLEETALAAFLSYCPGMGVALRMYPLKVTWWFCAFPYSLLIFIYDEVRKLILRRYPGGWVEKETYY

Mutation: 383H

Update README

Update the README to reflect the changes in deployment because of docker.

Fix integration test errors

There are errors in the integrations tests which need fixing. These tests haven't run for a long time, so they may be obsolete.

web frontend

Right now, hommod only has a rest api for building models. It could use a web frontend.

Exception: chain A occurs more than once after cleaning

HOPE gets this error back from hommod:

f551ff58-c277-6de1-376b-4f8830643b0f_HUMAN_40-263:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 929, in modelProc
    mainTargetSeq, mainDomainRange)
  File "/usr/src/app/hommod_rest/services/model.py", line 468, in _build_for_domain
    self._set_template (mainTemplateID.pdbac)
  File "/usr/src/app/hommod_rest/services/model.py", line 390, in _set_template
    raise Exception ("chain %s occurs more than once after cleaning" % chain)
Exception: chain A occurs more than once after cleaning

The position is 227 and the sequence is:

MPKKKPTPIQLNPAPDGSAVNGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFEK
ISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEIS
ICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAVIKGLTYLREKHKIMHRDVKPSNILVNSRGEIKLCDFG
VSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLSLVEMAVGRYPIPPPDAKELELMFGCQVE
GDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELLDYIVNEPPPKLPSGVFSLEFQDFVNKCLIKNPAERA
DLKQLMVHAFIKRSDAEEVDFAGWLCSTIGLNQPSTPTHAAGV

What does this error mean? Is this a bug in hommod or can't hommod do anything about it?

Mismatch between alignment and template sequence

The following error appeared in HOPE:

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 60, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 1014, in modelProc
    raise Exception("the following models have failed:\n" + s)
Exception: the following models have failed:
9a6424c4-4096-d62d-4150-e38ebec3799b_HUMAN_32-188_3UX9-A:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 944, in modelProc
    main_target_sequence, main_domain_range)
  File "/usr/src/app/hommod_rest/services/model.py", line 628, in _build_for_domain
    targetsInterproRanges, picker)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 439, in pickAlignments
    if picker.accepts(targetID, alignment):
  File "/usr/src/app/hommod_rest/services/interaction.py", line 80, in accepts
    sstart, send = get_target_covered_range(subjectChainAlignment, sseq)
  File "/usr/src/app/hommod_rest/services/modelutils.py", line 812, in get_target_covered_range
    % (alignment['template'], template_seq))
Exception: mismatch between alignment and template sequence:
IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSL
IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSLE

9a6424c4-4096-d62d-4150-e38ebec3799b_HUMAN_32-189_3UX9-A:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 944, in modelProc
    main_target_sequence, main_domain_range)
  File "/usr/src/app/hommod_rest/services/model.py", line 628, in _build_for_domain
    targetsInterproRanges, picker)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 439, in pickAlignments
    if picker.accepts(targetID, alignment):
  File "/usr/src/app/hommod_rest/services/interaction.py", line 80, in accepts
    sstart, send = get_target_covered_range(subjectChainAlignment, sseq)
  File "/usr/src/app/hommod_rest/services/modelutils.py", line 812, in get_target_covered_range
    % (alignment['template'], template_seq))
Exception: mismatch between alignment and template sequence:
IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSL
IVLTQPPSVSGAPGQRVTISCSGSSSNIGSNYVSWYQQLPGTAPKLLIYDNNQRPSGVPDRFSGSKSGTSASLAITGLQSEDEADYYCQVRDNNENEWVFGGGTKLTVLEVQLVESGGGLVQPGGSLRLSCAASGFTFSSYAMSWVRQAPGKGLEWVSAISGSGGSTYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCARYIDFGDHMDFWGQGTLVTVSSLE

@cbaakman, can you explain what the cause is before fixing it?

cannot connect to amqp

Right now when hommod runs, it repeatedly prints the following message:

celery_1    | [2017-03-03 15:58:58,391: ERROR/Beat] beat: Connection error: [Errno -2] Name or service not known. Trying again in 20.0 seconds...
celery_1    | [2017-03-03 15:59:18,407: ERROR/MainProcess] consumer: Cannot connect to amqp://guest:**@hommodrest_rabbitmq_1:5672//: [Errno -2] Name or service not known.
celery_1    | Trying again in 22.00 seconds...
celery_1    |

Also hommod returns 500 errors to all users

Prevent the same job from running twice

If the user submits the same data, a duplicate job will be started. How can we prevent this?

hope-flask has an implementation for this. Maybe it can be used here?

BLAST Database error: Could not find volume or alias file

HOPE gets the following error from hommod:

BLAST Database error: Could not find volume or alias file (/data/blast/uniprot_trembl) referenced in alias file (/data/blast/uniprot)

/srv/hommod on the host (chelonium in production) is mapped to /data in the docker containers; however, /srv/hommod doesn't contain the file shown in the error:

➜  ~ ls /srv/hommod 
blacklisted_templates  blast  fasta  interpro  models  tmp
➜  ~ ls /srv/hommod/blast 
templates.phr          uniprot_trembl.06.psq  uniprot_trembl.15.psq
templates.pin          uniprot_trembl.07.phr  uniprot_trembl.16.phr
templates.psq          uniprot_trembl.07.pin  uniprot_trembl.16.pin
uniprot.pal            uniprot_trembl.07.psq  uniprot_trembl.16.psq
uniprot_sprot.phr      uniprot_trembl.08.phr  uniprot_trembl.17.phr
uniprot_sprot.pin      uniprot_trembl.08.pin  uniprot_trembl.17.pin
uniprot_sprot.psq      uniprot_trembl.08.psq  uniprot_trembl.17.psq
uniprot_trembl.00.phr  uniprot_trembl.09.phr  uniprot_trembl.18.phr
uniprot_trembl.00.pin  uniprot_trembl.09.pin  uniprot_trembl.18.pin
uniprot_trembl.00.psq  uniprot_trembl.09.psq  uniprot_trembl.18.psq
uniprot_trembl.01.phr  uniprot_trembl.10.phr  uniprot_trembl.19.phr
uniprot_trembl.01.pin  uniprot_trembl.10.pin  uniprot_trembl.19.pin
uniprot_trembl.01.psq  uniprot_trembl.10.psq  uniprot_trembl.19.psq
uniprot_trembl.02.phr  uniprot_trembl.11.phr  uniprot_trembl.20.phr
uniprot_trembl.02.pin  uniprot_trembl.11.pin  uniprot_trembl.20.pin
uniprot_trembl.02.psq  uniprot_trembl.11.psq  uniprot_trembl.20.psq
uniprot_trembl.03.phr  uniprot_trembl.12.phr  uniprot_trembl.21.phr
uniprot_trembl.03.pin  uniprot_trembl.12.pin  uniprot_trembl.21.pin
uniprot_trembl.03.psq  uniprot_trembl.12.psq  uniprot_trembl.21.psq
uniprot_trembl.04.phr  uniprot_trembl.13.phr  uniprot_trembl.22.phr
uniprot_trembl.04.pin  uniprot_trembl.13.pin  uniprot_trembl.22.pin
uniprot_trembl.04.psq  uniprot_trembl.13.psq  uniprot_trembl.22.psq
uniprot_trembl.05.phr  uniprot_trembl.14.phr  uniprot_trembl.23.phr
uniprot_trembl.05.pin  uniprot_trembl.14.pin  uniprot_trembl.23.pin
uniprot_trembl.05.psq  uniprot_trembl.14.psq  uniprot_trembl.23.psq
uniprot_trembl.06.phr  uniprot_trembl.15.phr  uniprot_trembl.pal
uniprot_trembl.06.pin  uniprot_trembl.15.pin

Why isn't the file there?

Fix unit and integration tests

The unit and integration tests are failing. Fix them.

Exception: main domain range: 33 - 732 exceeds sequence length(721)

I get this error in HOPE. What does it mean? Can anything be done about it?

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 60, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 1014, in modelProc
    raise Exception("the following models have failed:\n" + s)
Exception: the following models have failed:
147b60cf-e161-6093-2b7f-390a5b952991_HUMAN_34-732_3LY6-A:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 944, in modelProc
    main_target_sequence, main_domain_range)
  File "/usr/src/app/hommod_rest/services/model.py", line 432, in _build_for_domain
    len(main_target_sequence)))
Exception: main domain range: 33 - 732 exceeds sequence length(721)

chain A in 1R6F occurs more than once after cleaning

The following job in HOPE fails because of the error below in hommod:

The sequence:

MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFDSDVNKLNVSQQPLLDVEGNLIKMHAADLEKPMVEKQDQSPSLRTGEEKKDVSISRLREAFSLRHTTENKPHSPKTPEPRRSPLGQKRGMLSSSTSGAISDKGVLRPQKEAVSSSHGPSDPTDRAEVEKDSGHGSTSVDSEGFSIPDTGSHCSSEYAASSPGDRGSQEHVDSQEKAPETDDSFSDVDCHSNQEDTGCKFRVLPQPTNLATPNTKRFKKEEILSSSDICQKLVNTQDMSASQVDVAVKINKKVVPLDFSMSSLAKRIKQLHHEAQQSEGEQNYRKFRAKICPGENQAAEDELRKEISKTMFAEMEIIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNEAVLIENLEIFRKNGFDFVIDENAPVTERAKLISLPTSKNWTFGPQDVDELIFMLSDSPGVMCRPSRVKQMFASRACRKSVMIGTALNTSEMKKLITHMGEMDHPWNCPHGRPTMRHIANLGVISQN

Mutation: P470S

The template:

{'file_path': None, 'template': {'required_identity': 23.28984896457817, 'ac_code': '1R6F', 'chain': 'A', 'identity': 44}}

The exception is:

        Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hope/factory.py", line 171, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hope/tasks.py", line 233, in get_structure_features
    model = modeler.from_sequence(sequence, position, template_id)
  File "/usr/src/app/hope/domain/modeler.py", line 12, in from_sequence
    template_id)
  File "/usr/src/app/hope/services/hommod.py", line 68, in run
    raise ServiceError(json.loads(r.text)['message'])
hope.services.types.ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 38, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 849, in modelProc
    self._set_template(chosenTemplateID.pdbac)
  File "/usr/src/app/hommod_rest/services/model.py", line 412, in _set_template
    raise Exception("chain %s in %s occurs more than once after cleaning" % (chain, tempac))
Exception: chain A in 1R6F occurs more than once after cleaning

How can we build models periodically?

The purpose of hommod-rest is to have models ready so that services don't need to wait a long time for them to be built. In order to do this, hommod-rest must trigger the building/updating of models by itself.

How can we do this? One idea is to use celery's periodic tasks.

Allow the client to specify the template to use

Allow clients to specify which template should be used to create the model, bypassing the BLAST search done at the beginning.

This is required for issue https://github.com/cmbi/hope-flask/issues/303 in HOPE. Coos posted the following comment in that discussion:

Right now hommod's organizes models by naming them after their input sequence, species and covered range. If hommod is to take a template id as input, the model storage system would have to change, because there would be an extra parameter. There can then be two different models for the same piece of protein, differing by template only.

...and...

Hommod blasts for a template by itself, it forces yasara to use the found template. Yes, it's possible to tell yasara which template it should take!

We need to discuss what changes would need to be made to the storage system.

How should the result be returned

Currently the result is a json formatted response containing:

Alignment sequences
PDB file content
Information such as the template

This response is quite large. Is it better to just return the zipped model result? Is there a another option?

Dockerfile java8

It should be possible to install java 8 in the docker image using apt. Because it's version 14.04 this might be via another package repository (e.g on launchpad) or via backports. This needs looking into.

Exception: alignment not provided for interacting chain B

Another error from hommod when using HOPE:

Exception: the following models have failed:
6dd7080c-8fdb-6b4d-993d-75bfe3060c94_HUMAN_13-1488:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 927, in modelProc
    mainTargetSeq, mainDomainRange)
  File "/usr/src/app/hommod_rest/services/model.py", line 636, in _build_for_domain
    yasaraChains, interactingChainAlignments)
  File "/usr/src/app/hommod_rest/services/interaction.py", line 98, in __init__
    "interacting chain %s" % chainID)
Exception: alignment not provided for interacting chain B

Quiet output when generating image

Docker image generation results in a 48MB log file. Commands like tar can be made less verbose to shrink this substantially.

ValueError: /deps/yasara/yasara/ not found

The following error is returned when called from HOPE during get_structure_features:

        Traceback (most recent call last):
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hope/factory.py", line 171, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python3.5/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hope/tasks.py", line 206, in get_structure_features
    model = modeler.from_sequence(target_seq, position)
  File "/usr/src/app/hope/domain/modeler.py", line 14, in from_sequence
    model = modeling_service.run(target_sequence, position, 'HUMAN')
  File "/usr/src/app/hope/services/hommod.py", line 66, in run
    raise ServiceError(json.loads(r.text)['message'])
hope.services.types.ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 35, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 778, in modelProc
    self._check_init()
  File "/usr/src/app/hommod_rest/services/model.py", line 226, in _check_init
    self.yasara_dir = flask_app.config ['YASARADIR']
  File "/usr/src/app/hommod_rest/services/model.py", line 210, in yasara_dir
    raise ValueError("{} not found".format (yasara_dir))
ValueError: /deps/yasara/yasara/ not found

This is possibly related to #11.

TypeError: 'BlastAlignment' object has no attribute 'getitem'

I get the following error from hommod in hope. The input to HOPE is:

MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD

The mutation is E349R.

ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 33, in create_model
    paths = modeler.modelProc (sequence, species_id, residue_number, False)
  File "/usr/src/app/hommod_rest/services/model.py", line 815, in modelProc
    domainalign.getAlignments (ranges, mainTargetSeq)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 734, in getAlignments
    alignment, pid, pcover)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 560, in _get_range_from
    m = getCoveredTargetRange(alignment)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 435, in getCoveredTargetRange
    while not alignment['target'][targetStart].isalpha():
TypeError: 'BlastAlignment' object has no attribute '__getitem__'

Exception: No template blast hit syntax

I got the following error from hommod when using HOPE.

ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 33, in create_model
    paths = modeler.modelProc (sequence, species_id, residue_number, False)
  File "/usr/src/app/hommod_rest/services/model.py", line 815, in modelProc
    domainalign.getAlignments (ranges, mainTargetSeq)
  File "/usr/src/app/hommod_rest/services/domainalign.py", line 701, in getAlignments
    pdbid, pdbchain = getTemplatePDBIDandChain(hitID)
  File "/usr/src/app/hommod_rest/services/modelutils.py", line 329, in getTemplatePDBIDandChain
    raise Exception("No template blast hit syntax: \'%s\'" % blastHitID)
Exception: No template blast hit syntax: 'pdb|4KZZ|g'

Error when template id is None

When the template id is None, the following error happens:

TypeError: argument of type 'NoneType' is not iterable

Please write some unit tests for the new template parameter.

multimer interfaces

When proteins from multimer complexes, it's important to preserve the multimer interface when modeling. However, this domain is sometimes missing.

We must make hommod look at alternatives in such a case.

ZeroDivisionError: integer division or modulo by zero

HOPE gets this error from HOMMOD:

hope.services.types.ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 38, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 849, in modelProc
    self._set_template(chosenTemplateID.pdbac)
  File "/usr/src/app/hommod_rest/services/model.py", line 416, in _set_template
    return [tempobj, nMolsOligomerized / nMolsUnoligomerized]
ZeroDivisionError: integer division or modulo by zero

Create a test for this first. Whenever the denominator is a variable you should always check that it's not zero. I'm not sure if that should be possible but I suspect that it's normal for zero mols to be unoligomerized.

The input sequence is:

MMSFVQKGSWLLLALLHPTIILAQQEAVEGGCSHLGQSYADRDVWKPEPCQICVCDSGSVLCDDIICDDQELDCPNPEIPFGECCAVCPQPPTAPTRPPNGQGPQGPKGDPGPPGIPGRNGDPGIPGQPGSPGSPGPPGICESCPTGPQNYSPQYDSYDVKSGVAVGGLAGYPGPAGPPGPPGPPGTSGHPGSPGSPGYQGPPGEPGQAGPSGPPGPPGAIGPSGPAGKDGESGRPGRPGERGLPGPPGIKGPAGIPGFPGMKGHRGFDGRNGEKGETGAPGLKGENGLPGENGAPGPMGPRGAPGERGRPGLPGAAGARGNDGARGSDGQPGPPGPPGTAGFPGSPGAKGEVGPAGSPGSNGAPGQRGEPGPQGHAGAQGPPGPPGINGSPGGKGEMGPAGIPGAPGLMGARGPPGPAGANGAPGLRGGAGEPGKNGAKGEPGPRGERGEAGIPGVPGAKGEDGKDGSPGEPGANGLPGAAGERGAPGFRGPAGPNGIPGEKGPAGERGAPGPAGPRGAAGEPGRDGVPGGPGMRGMPGSPGGPGSDGKPGPPGSQGESGRPGPPGPSGPRGQPGVMGFPGPKGNDGAPGKNGERGGPGGPGPQGPPGKNGETGPQGPPGPTGPGGDKGDTGPPGPQGLQGLPGTGGPPGENGKPGEPGPKGDAGAPGAPGGKGDAGAPGERGPPGLAGAPGLRGGAGPPGPEGGKGAAGPPGPPGAAGTPGLQGMPGERGGLGSPGPKGDKGEPGGPGADGVPGKDGPRGPTGPIGPPGPAGQPGDKGEGGAPGLPGIAGPRGSPGERGETGPPGPAGFPGAPGQNGEPGGKGERGAPGEKGEGGPPGVAGPPGGSGPAGPPGPQGVKGERGSPGGPGAAGFPGARGLPGPPGSNGNPGPPGPSGSPGKDGPPGPAGNTGAPGSPGVSGPKGDAGQPGEKGSPGAQGPPGAPGPLGIAGITGARGLAGPPGMPGPRGSPGPQGVKGESGKPGANGLSGERGPPGPQGLPGLAGTAGEPGRDGNPGSDGLPGRDGSPGGKGDRGENGSPGAPGAPGHPGPPGPVGPAGKSGDRGESGPAGPAGAPGPAGSRGAPGPQGPRGDKGETGERGAAGIKGHRGFPGNPGAPGSPGPAGQQGAIGSPGPAGPRGPVGPSGPPGKDGTSGHPGPIGPPGPRGNRGERGSEGSPGHPGQPGPPGPPGAPGPCCGGVGAAAIAGIGGEKAGGFAPYYGDEPMDFKINTDEIMTSLKSVNGQIESLISPDGSRKNPARNCRDLKFCHPELKSGEYWVDPNQGCKLDAIKVFCNMETGETCISANPLNVPRKHWWTDSSAEKKHVWFGESMDGGFQFSYGNPELPEDVLDVQLAFLRLLSSRASQNITYHCKNSIAYMDQASGNVKKALKLMGSNEGEFKAEGNSKFTYTVLEDGCTKHTGEWSKTVFEYRTRKAVRLPIVDIAPYDIGGPDQEFGVDVGPVCF

And the template is: {'file_path': None, 'template': {'required_identity': 19.5, 'ac_code': '3HQV', 'chain': 'A', 'identity': 582}}

Refactor services/model.py

The functions in this file are very long and hard to test. Refactor.

Locking Interpro jobs

To provide itself with interpro data, hommod runs interpro jobs during a modelling job. When two jobs need the same interpro file however, only one interpro job should run.

Right now this is solved by using lock files. Might there be a cleaner alternative?

Model couldn't be built

I get the feeling that Hommod is less able to build models for HOPE than the old solution. Many more reports are "empty" because there's no structure. This is a feeling, so we need to first check if this is the case.

Are there any reports where we expect a model to be built. The template should be shown on the admin page for the report
What is the reason that Hommod cannot create a model? Currently HOPE only gets the message "Hommod couldn't create a model". It'd be useful to give a reason.

Once we answer these questions, we can decide what to do about it, if anything.

@hvenselaar Would you be able to look at point 1?
@cbaakman Would you be able to look at point 2?

Cache downloaded templates

Hommod needs to access template files (pdb structures) multiple times each modeling run. This can be with intervals of seconds.

Currently, hommod re-downloads the pdb structure with each new step that uses it. But I think it would be faster to have a pdb service in hommod that handles the request for a template file and downloads it only once per modeling run.

AttributeError: 'TemplateID' object has no attribute 'chain'

HOPE gets the following error when trying to create a model with hommod:

Exception: the following models have failed:
e8ccf04f-7409-2342-9f5d-9b80a1d99517_HUMAN_71-194_1UB1-A:
Traceback (most recent call last):
  File "/usr/src/app/hommod_rest/services/model.py", line 951, in modelProc
    mainTargetSeq, mainDomainRange)
  File "/usr/src/app/hommod_rest/services/model.py", line 472, in _build_for_domain
    mainTemplateID.chain))
AttributeError: 'TemplateID' object has no attribute 'chain'

Position is: 143
Template is: 1UB1_A
Sequence is:

MVAGMLGLREEKSEDQDLQGLKDKPLKFKKVKKDKKEEKEGKHEPVQPSAHHSAEPAEAGKAETSEGSGSAPAVPEASASPKQRRSIIRDRGPMYDDPTLPEGWTRKLKQRKSGRSAGKYDVYLINPQGKAFRSKVELIAYFEKVGDTSLDPNDFDFTVTGRGSPSRREQKPPKKPKSPKAPGTGRGRGRPKGSGTTRPKAATSEGVQVKRVLEKSPGKLLVKMPFQTSPGGKAEGGGATTSTQVMVIKRPGRKRKAEADPQAIPKKRGRKPGSVVAAAAAEAKKKAVKESSIRSVQETVLPIKKRKTRETVSIEVKEVVKPLLVSTLGEKSGKGLKTCKSPGRKSKESSPKGRSSSASSPPKKEHHHHHHHSESPKAPVPLLPPLPPPPPEPESSEDPTSPPEPQDLSSSVCKEEKMPRGGSLESDGCPKEPAKTQPAVATAATAAEKYKHRGEGERKDIVSSSMPRPNREEPVDSRTPVTERVS

Connection to YASARA broken

HOPE received the following error from HOMMOD:

hope.services.types.ServiceError: Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 38, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 849, in modelProc
    self._set_template(chosenTemplateID.pdbac)
  File "/usr/src/app/hommod_rest/services/model.py", line 387, in _set_template
    self.yasara.CleanObj(tempobj)
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 2338, in CleanObj
    run(command[:-1])
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 1012, in run
    if (command.find("\n")==-1): return(process("EXECUTE",command))
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 1006, in process
    result=com.receivemessage(com.RESULT)
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 739, in receivemessage
    (messagetype,datasize)=struct.unpack('ii',self.receive(8))
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 722, in receive
    if (len(chunk)==0): self.reportbrokenconn()
  File "/deps/yasara/yasara/pym/yasaramodule.py", line 692, in reportbrokenconn
    raise RuntimeError("Connection to YASARA broken. Either you exited YASARA manually or it encountered a fatal error")
RuntimeError: Connection to YASARA broken. Either you exited YASARA manually or it encountered a fatal error

The following template was used: {'file_path': None, 'template': {'required_identity': 19.5, 'ac_code': '3JBH', 'chain': 'A', 'identity': 216}}

This is likely a bug in yasara but it would be nice to know the cause before we email Elmar.

YASARA Version 15.3.8.L detected error 728: The connection to the Python module failed with error code 4.

and

Fatal error while trying to exit. It is possible that the scene could not be saved. Original error 728, subsequent error 39.
New error details: ysu_exit: Failed to get directory

Update dockerfiles to match hope-flask

Update the dockerfiles to match hope-flask. This allows a separate production and development environment, and supports running tests in docker.

Exception: inteproscan job timed out

I get the following error in HOPE from hommod.

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 240, in trace_task
    R = retval = fun(*args, **kwargs)
  File "/usr/src/app/hommod_rest/factory.py", line 96, in __call__
    return TaskBase.__call__(self, *args, **kwargs)
  File "/usr/local/lib/python2.7/site-packages/celery/app/trace.py", line 438, in __protected_call__
    return self.run(*args, **kwargs)
  File "/usr/src/app/hommod_rest/tasks.py", line 60, in create_model
    template_id)
  File "/usr/src/app/hommod_rest/services/model.py", line 786, in modelProc
    ranges = interpro.get_domain_locations(main_target_sequence)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 181, in get_domain_locations
    filepath = self._create_data_file(sequence)
  File "/usr/src/app/hommod_rest/services/interpro.py", line 164, in _create_data_file
    raise Exception("inteproscan job timed out")
Exception: inteproscan job timed out

How long is the timeout and can we do anything to prevent this causing issue in HOPE?