FAQ¶

ValueError: Shape of passed values is (13933, 1796), indices imply (14, 1796)¶

If you get an error like the following after upgrading to GimmeMotifs >=0.15, you can fix it by deleting the GimmeMotifs cache directory ~/.cache/gimmemotifs.

Traceback (most recent call last):
File "/home/simon/anaconda3/envs/gimme-0.15.1/bin/gimme", line 11, in <module>
    cli(sys.argv[1:])
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/gimmemotifs/cli.py", line 661, in cli
    args.func(args)
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/gimmemotifs/commands/maelstrom.py", line 33, in maelstrom
    run_maelstrom(
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/gimmemotifs/maelstrom.py", line 343, in run_maelstrom
    counts = scan_regionfile_to_table(
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 164, in scan_regionfile_to_table
    s.set_threshold(fpr=FPR)
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/gimmemotifs/scanner.py", line 958, in set_threshold
    self._threshold = pd.concat((self._threshold, df), axis=1)
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 287, in concat
    return op.get_result()
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/pandas/core/reshape/concat.py", line 502, in get_result
    new_data = concatenate_block_managers(
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/pandas/core/internals/concat.py", line 84, in concatenate_block_managers
    return BlockManager(blocks, axes)
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 149, in __init__
    self._verify_integrity()
File "/home/simon/anaconda3/envs/gimme-0.15.1/lib/python3.8/site-packages/pandas/core/internals/managers.py", line 326, in _verify_integrity
    raise construction_error(tot_items, block.shape[1:], self.axes)
ValueError: Shape of passed values is (13933, 1796), indices imply (14, 1796)

SQLite error when running on a cluster¶

The current implementation of the cache that GimmeMotifs uses does not play nice with concurrent access, for instance on a cluster. The result is that the cache will get corrupted and that GimmeMotifs will fail. Until this is fixed, there is a workaround. In your job submission script, use something like the following:

NEW_CACHE=$TMPDIR/cache
mkdir -p $NEW_CACHE
if [ -z $XDG_CACHE_HOME ]; then
    XDG_CACHE_HOME=$HOME/.cache
fi
cp -r $XDG_CACHE_HOME/gimmemotifs $NEW_CACHE/
export XDG_CACHE_HOME=$NEW_CACHE
echo 'Using $XDG_CACHE_HOME for cache'

This will use a local directory to store the cache.

ImportError: dlopen: cannot load any more object with static TLS¶

This is a bug that will occur on Ubuntu 16.04 (Trusty). The recommended solution is to upgrade Ubuntu as Trusty is no longer supported. However, if you are unable to do so, there is a workaround. Run the following command:

$ export LD_PRELOAD=$CONDA_PREFIX/lib/libgomp.so

Now you should be able to run gimme as normal.

‘i’ format requires -2147483648 <= number <= -2147483646¶

If you get the following error with gimme maelstrom:

` 'i' format requires -2147483648 <= number <= -2147483646 `

this means that you should decrease the amount of input sequences. It is a bug that should be solved with a newer version of Python. However, it might be bestg anyway to use a limited set of sequences (< ~100k) as input.

Sorry, motif prediction tool [X] is not supported¶

If gimme motifs does not recognize a motif tools that should be installed, you can update the configuration file. This file is likely located at ~/.config/gimmemotifs/gimmemotifs.cfg.

Edit this file and update the following lines under the [params] section:

available_tools = MDmodule,MEME,MEMEW,Weeder,GADEM,MotifSampler,Trawler,Improbizer,BioProspector,Posmo,ChIPMunk,AMD,HMS,Homer
tools = MDmodule,MEME,Weeder,MotifSampler,trawler,Improbizer,BioProspector,Posmo,ChIPMunk,AMD,Homer

Add the tool that you want to the available_tools parameter. Keep in mind the exact upper-/lower-case combination that GimmeMotifs uses. By updating the tools parameter you can set the tools that gimme motifs uses by default. This can always be changed at the command-line.

In addition, you might also have to update the binary location. Either update this section if it exists or add it. For instance, to set this information for MEME:

[MEME]
bin = /home/simon/anaconda2/envs/gimme/gimmemotifs/tools/meme.bin
dir = /home/simon/anaconda2/envs/gimme/gimmemotifs/tools

The dir variable ususally doesn’t matter and you can set it the same directory as where the binary is located.

I get motifs that have differential scores in gimme maelstrom, however, the number is not different across clusters¶

The different methods use different ways to rank the motifs. The hypergeometric test is the only one that uses motif counts. All the other methods use the PWM logodds score of the best match. While the counts may not be different across clusters, the scores most likely are.

I have upgraded GimmeMotifs and now it doesn’t find my genome¶

The genome index in GimmeMotifs has changed, see Upgrading from 0.11.1.

I cannot run gimme index anymore¶

The genome index in GimmeMotifs has changed, see Upgrading from 0.11.1.

I get ‘RuntimeError: Invalid DISPLAY variable’¶

The default matplotlib configuration expects a display. Probably you are running GimmeMotifs on a server without an X server. There are several ways to solve it.

Option 1¶

Change the matplotlib configuration. Find the path of the matplotlib installation of your current environment (make sure to activate the environment you use for GimmeMotifs first).

$ python -c "import matplotlib; print(matplotlib.__file__)"
/home/simon/anaconda2/envs/gimme3/lib/python3.5/site-packages/matplotlib/__init__.py

So, matplotlib is in /home/simon/anaconda2/envs/gimme3/lib/python3.5/site-packages/matplotlib/. Now you can edit <MATPLOT_DIR>/mpl-data/matplotlibrc. In my example case this would be:

/home/simon/anaconda2/envs/gimme3/lib/python3.5/site-packages/matplotlib/mpl-data/matplotlibrc

Change the line

backend     : Qt5Agg

backend     : Agg

You can also put a matplotlibrc file in $HOME/.config/matplotlib.

Option 2¶

Run GimmeMotifs via xvfb-run. If this program is installed, you can simply run GimmeMotifs in a virtual X server environment.

For example:

$ xvfb-run gimme motifs [args]

I get a KeyError when running gimme maelstrom¶

You get an error like this:

File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc (pandas/_libs/index.c:5280)
File "pandas/_libs/index.pyx", line 154, in pandas._libs.index.IndexEngine.get_loc (pandas/_libs/index.c:5126)
File "pandas/_libs/hashtable_class_helper.pxi", line 1210, in pandas._libs.hashtable.PyObjectHashTable.get_item (pandas/_libs/hashtable.c:20523)
File "pandas/_libs/hashtable_class_helper.pxi", line 1218, in pandas._libs.hashtable.PyObjectHashTable.get_item (pandas/_libs/hashtable.c:20477)
KeyError: '5'

This a bug in gimme maelstrom. The column headers can’t be numbers. Change this to a word, for instance cluster5 or col5.