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just annotate it, dammit!
http://dib-lab.github.io/dammit/
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ValueError: cannot convert float NaN to integer #78

Closed johnsolk closed 7 years ago

johnsolk commented 8 years ago

Seems like a numpy problem? Encountered with command (NO user-defined db):

dammit annotate MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta --busco-group eukaryota --n_threads 4
camillescott commented 8 years ago

Hmm. Could you copy that transcriptome to a folder I have access to on the HPCC? Looks like a problem with my GFF3 parser and pandas.

On Wed, Nov 2, 2016 at 9:05 PM, Lisa Cohen notifications@github.com wrote:

Seems like a numpy problem? Encountered with command:

dammit annotate MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta --busco-group eukaryota --n_threads 4

  • fasta-annotate:/mnt/home/ljcohen/dammit_results/ MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit/ MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit.fasta:
    • Python: function get_annotate_fasta_task.annotate_fasta ######################################## TaskError - taskid:fasta-annotate:/mnt/home/ljcohen/dammit_results/ MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit/ MMETSP0398.trinity_out_2.2.0.Trinity.fixed.fasta.dammit.fasta PythonAction Error Traceback (most recent call last): File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/site-packages/doit/action.py", line 383, in execute returned_value = self.py_callable(_self.args, *_kwargs) File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/ site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 88, in annotate_fasta df) File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/ site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in generate_sequencesummary for , row in fgroup.iterrows()]) File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/ site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in for _, row in fgroup.iterrows()]) ValueError: cannot convert float NaN to integer

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Camille Scott

Graduate Group for Computer Science Lab for Data Intensive Biology University of California, Davis

camille.scott.w@gmail.com

johnsolk commented 8 years ago

Thank you, here you go:

/mnt/research/ged/data/dammit_MMETSP0398_results
johnsolk commented 7 years ago

same error on ucd farm cluster, different transcriptome (w user-defined db):

full command:

dammit annotate p_ast2016.fasta --user-databases past_PRO.fas --busco-group metazoa --n_threads 4
- [ ] fasta-annotate:/home/ljcohen/P_astreoides/p_ast2016.fasta.dammit/p_ast2016.fasta.dammit.fasta:
    * Python: function get_annotate_fasta_task.annotate_fasta
########################################
TaskError - taskid:fasta-annotate:/home/ljcohen/P_astreoides/p_ast2016.fasta.dammit/p_ast2016.fasta.dammit.fasta
PythonAction Error
Traceback (most recent call last):
  File "/home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/doit-0.29.0-py3.5.egg/doit/action.py", line 383, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 88, in annotate_fasta
    df)
  File "/home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in generate_sequence_summary
    for _, row in fgroup.iterrows()])
  File "/home/ljcohen/anaconda2/envs/py3.dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in <listcomp>
    for _, row in fgroup.iterrows()])
ValueError: cannot convert float NaN to integer
johnsolk commented 7 years ago

This also happens with the provided test transcriptome (w user-defined db):

dammit annotate cdna_nointrons_utrs.fa --user-databases pep.fa --busco-group eukaryota --n_threads 4
- [ ] fasta-annotate:/mnt/home/ljcohen/dammit_test/cdna_nointrons_utrs.fa.dammit/cdna_nointrons_utrs.fa.dammit.fasta: 
    * Python: function get_annotate_fasta_task.annotate_fasta
########################################
TaskError - taskid:fasta-annotate:/mnt/home/ljcohen/dammit_test/cdna_nointrons_utrs.fa.dammit/cdna_nointrons_utrs.fa.dammit.fasta
PythonAction Error
Traceback (most recent call last):
  File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/site-packages/doit/action.py", line 383, in execute
    returned_value = self.py_callable(*self.args, **kwargs)
  File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 88, in annotate_fasta
    df)
  File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in generate_sequence_summary
    for _, row in fgroup.iterrows()])
  File "/mnt/home/ljcohen/.conda/envs/dammit/lib/python3.5/site-packages/dammit-1.0.dev0-py3.5.egg/dammit/tasks/report.py", line 44, in <listcomp>
    for _, row in fgroup.iterrows()])
ValueError: cannot convert float NaN to integer
camillescott commented 7 years ago

Fixed in refactor branch, closing.