genemark prediction mistake crashes pyhmmer #28
Description
[Sep 11 02:47 AM] Measuring assembly completeness with buscolite [lineage=metazoa_odb12] for all ab initio predictions
Traceback (most recent call last):
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/bin/funannotate2", line 7, in <module>
sys.exit(main())
^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/funannotate2/__main__.py", line 26, in main
predict(args)
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/funannotate2/predict.py", line 576, in predict
d, m, stats, cfg = runbusco(
^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/buscolite/busco.py", line 512, in runbusco
if isinstance(r.result(), list):
^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/concurrent/futures/_base.py", line 449, in result
return self.__get_result()
^^^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/concurrent/futures/_base.py", line 401, in __get_result
raise self._exception
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/concurrent/futures/thread.py", line 59, in run
result = self.fn(*self.args, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/buscolite/search.py", line 640, in hmmer_search
for top_hits in pyhmmer.hmmsearch([hmm], sequences):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_base.py", line 483, in _multi_threaded
raise e
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_base.py", line 469, in _multi_threaded
result = results[0].get() # <-- blocks until result is available
^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_base.py", line 146, in get
raise self.result
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_base.py", line 293, in run
hits = self.process(chore.query)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_base.py", line 325, in process
hits = self.query(query)
^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/utils.py", line 70, in _method
return method.__get__(obj, cls)(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lustre1/project/stg_00002/mambaforge/vsc37429/envs/funannotate2/lib/python3.12/site-packages/pyhmmer/hmmer/_hmmsearch.py", line 44, in _
return self.pipeline.search_hmm(query, self.targets)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pyhmmer/plan7.pyx", line 5750, in pyhmmer.plan7.Pipeline.__pyx_fuse_0_1search_hmm
File "pyhmmer/plan7.pyx", line 5813, in pyhmmer.plan7.Pipeline.search_hmm
ValueError: sequence length over comparison pipeline limit (100000)
I encountered an edgecase where genemark predict a gene with a coding sequence longer than 100,000 amino acids. After removing this sequence from predictions.genemark.gff3 and rerunning funannotate 2 predict the pipeline finishes without issues. Perhaps a check for valid gene predictions prior to pyhmmer could help prevent this.