ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif'

[chuyaowang]

I have encountered this error:

ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif' (/opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/gimmemotifs/motif/__init__.py)

This happened after I ran pip uninstall gimmemotifs and conda install -c bioconda gimmemotifs in an attempt to resolve the killed kernel issue. The installation was smooth, but gimmemotifs no longer works.

The killed kernel issue happened when I was running tfi.scan(fpr=0.02, motifs=None, verbose=True). The progress bar stayed at 0 for about 1 hour. I checked my CPU usage and found it very low, so I thought my kernel must have been killed. On my machine I have 16 GB of RAM and 16 GB of swap disk, could it be a memory issue? My data have about 17000 peaks and uses the hg38 reference genome and the default vertebrate motifs.

Here is full error report:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[2], line 1
----> 1 import celloracle as co
      2 from celloracle import motif_analysis as ma
      3 from celloracle.utility import save_as_pickled_object

File /opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/celloracle/__init__.py:8
      5 import warnings
      6 import logging
----> 8 from . import utility, network, network_analysis, go_analysis, data, data_conversion, oracle_utility
      9 from .trajectory.oracle_core import Oracle
     10 from .network import Net

File /opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/celloracle/utility/__init__.py:18
      7 from .make_log import makelog
      9 from .utility import (save_as_pickled_object, load_pickled_object,
     10                       intersect,
     11                       exec_process,
   (...)
     16                       knn_data_transferer,
     17                       update_adata)
---> 18 from .load_hdf5 import load_hdf5
     20 from .pandas_utility_for_jupyternotebook import init_datatable_mode
     22 from .package_version_checker import check_python_requirements

File /opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/celloracle/utility/load_hdf5.py:8
      6 from ..network import load_net
      7 from ..trajectory.oracle_core import load_oracle
----> 8 from ..motif_analysis.tfinfo_core import load_TFinfo
      9 from ..applications.differentiation_flow import load_gradient
     11 def load_hdf5(file_path, object_class_name=None):

File /opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/celloracle/motif_analysis/__init__.py:13
     11 from .motif_analysis_utility import is_genome_installed
     12 from .process_bed_file import peak2fasta, read_bed, remove_zero_seq, check_peak_format
---> 13 from .tfinfo_core import (load_TFinfo, load_TFinfo_from_parquets,
     14                           make_TFinfo_from_scanned_file, TFinfo, scan_dna_for_motifs)
     15 from .reference_genomes import SUPPORTED_REF_GENOME
     16 from .tss_annotation import get_tss_info

File /opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/celloracle/motif_analysis/tfinfo_core.py:36
     33 from genomepy import Genome
     35 from gimmemotifs.motif import Motif
---> 36 from gimmemotifs.motif import default_motifs
     37 from gimmemotifs.scanner import Scanner
     39 from ..utility.hdf5_processing import dump_hdf5, load_hdf5

ImportError: cannot import name 'default_motifs' from 'gimmemotifs.motif' (/opt/miniconda3/envs/celloracle/lib/python3.10/site-packages/gimmemotifs/motif/__init__.py)

[PedroMBarcelos]

Hello, I am having the same problem.
I downgraded to gimmemotifs 0.14.4 and it was able to import, but the kernel problem persisted.
Did you find a solution?

[baoa2ta]

Hi I am having the same issue where python keeps killing the process when running tfi.scan(fpr=0.02, motifs=None, verbose=True). My process bar runs to 100% then gets killed. I'm using the default motif set and have 25k peaks. Anyone has the solution?