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vanheeringen-lab / ANANSE

Prediction of key transcription factors in cell fate determination using enhancer networks. See full ANANSE documentation for detailed installation instructions and usage examples.
http://anansepy.readthedocs.io
MIT License
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Error using custom PWM #215

Open fmarletaz opened 5 months ago

fmarletaz commented 5 months ago

Hello,

I experienced a problem after using a custom database generate using gimme motif2fact (see below). I checked the files and they seem fine. Do you have any idea? Thanks a lot (and also for developing such a nice tool)! 

2024-04-24 10:02:46 | INFO | Loading specified motif file: Pargot_m2f/Pgot_OvL0Qm.gimme.vertebrate.v5.0.pfm
2024-04-24 10:02:57 | INFO |   Using motifs for 387 factors
2024-04-24 10:03:02 | ERROR | An error has been caught in function '<module>', process 'MainProcess' (4363), thread 'MainThread' (139841444013888):
Traceback (most recent call last):

> File "/home/ferdi/miniconda3/envs/ananse/bin/ananse", line 609, in <module>
    args.func(args)
    │    │    └ Namespace(atac_bams=['Chaetognath_ATAC_Larva_24_02_19_S12.srt.bam'], histone_bams=None, cage_tpms=None, genome='genomes/Pgot_...
    │    └ <function binding at 0x7f2b04162e60>
    └ Namespace(atac_bams=['Chaetognath_ATAC_Larva_24_02_19_S12.srt.bam'], histone_bams=None, cage_tpms=None, genome='genomes/Pgot_...
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/commands/binding.py", line 9, in binding
    predict_peaks(
    └ <function predict_peaks at 0x7f2b04161f30>
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/peakpredictor.py", line 1108, in predict_peaks
    p = PeakPredictor(
        └ <class 'ananse.peakpredictor.PeakPredictor'>
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/peakpredictor.py", line 98, in __init__
    self._load_motifs(factors=factors)
    │    │                    └ None
    │    └ <function PeakPredictor._load_motifs at 0x7f2b041612d0>
    └ <ananse.peakpredictor.PeakPredictor object at 0x7f2f5f3d3c40>
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/peakpredictor.py", line 151, in _load_motifs
    self._jaccard_motif_graph(indirect, factors)
    │    │                    │         └ None
    │    │                    └ True
    │    └ <function PeakPredictor._jaccard_motif_graph at 0x7f2b041613f0>
    └ <ananse.peakpredictor.PeakPredictor object at 0x7f2f5f3d3c40>
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/peakpredictor.py", line 211, in _jaccard_motif_graph
    reference_orthologs = self._load_factor2motifs()
                          │    └ <function PeakPredictor._load_factor2motifs at 0x7f2b04161360>
                          └ <ananse.peakpredictor.PeakPredictor object at 0x7f2f5f3d3c40>
  File "/home/ferdi/miniconda3/envs/ananse/lib/python3.10/site-packages/ananse/peakpredictor.py", line 182, in _load_factor2motifs
    raise ValueError(

ValueError: Zero factors remain after filtering the motif2factors.txt associated with pfmfile!