Error running Dogcatcher

[rresendepinto]

When running 2.0_Dogatcher.py, I get the following error :

Traceback (most recent call last): File "Dogcatcher/2.0_Dogcatcher.py", line 896, in last_time = time.time() File "/opt/conda/lib/python2.7/site-packages/pandas/core/frame.py", line 2927, in getitem indexer = self.columns.get_loc(key) File "/opt/conda/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'DOG_length'

Do you know what is causing this error? Thanks, Rui

[StellamarisSoares]

I have a similar problem with the mouse data. If you have found a solution, please tell me. Thank you!

[rresendepinto]

Hello! It is a problem with the fields in the output table which were changed in a bedtools update. You can use a docker image I created (rrpinto/dogcatcher). Hope that solves the issue! Best, Rui

[StellamarisSoares]

@rresendepinto Thank you for your answer. Unfortunately, I didn't find the docker image. Can you send the link?

[rresendepinto]

Hi, this is the link (https://hub.docker.com/r/rrpinto/dogcatcher), you can pull it using docker pull rrpinto/dogcatcher

[StellamarisSoares]

Thanks for that, but unfortunately, I still have the same error whether or not using the docker image.

Traceback (most recent call last): File "/Dogcatcher/2.0_Dogcatcher.py", line 887, in df = df [ df['DOG_length'] > window_size] #PLU Get only sections where the run on length is bigger than the base window File "/opt/conda/lib/python2.7/site-packages/pandas/core/frame.py", line 2927, in getitem indexer = self.columns.get_loc(key) File "/opt/conda/lib/python2.7/site-packages/pandas/core/indexes/base.py", line 2659, in get_loc return self._engine.get_loc(self._maybe_cast_indexer(key)) File "pandas/_libs/index.pyx", line 108, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/index.pyx", line 132, in pandas._libs.index.IndexEngine.get_loc File "pandas/_libs/hashtable_class_helper.pxi", line 1601, in pandas._libs.hashtable.PyObjectHashTable.get_item File "pandas/_libs/hashtable_class_helper.pxi", line 1608, in pandas._libs.hashtable.PyObjectHashTable.get_item KeyError: 'DOG_length'

[Erinico233]

Whether using the bedtools version recommended by the author or version 2.29.2, the commands used for generating BedGraph files were as follows:

bedtools genomecov -bg -split -strand + -ibam file1.bam -g chromsizes.genome > file1_plu.BedGraph
bedtools genomecov -bg -split -strand - -ibam file1.bam -g chromsizes.genome > file1_min.BedGraph

The resulting format of the generated BedGraph files looked something like this:

chr1    14764    14914    1
chr1    138450    138599    1
chr1    353918    354067    1
chr1    361855    362005    1
chr1    364138    364288    1
chr1    564602    564603    1

Afterwards, to adapt the BedGraph files for compatibility with the provided code, the 'chr' prefix was removed using the following commands:

sed -i 's/^chr//' ${BEDPATH}/${id}_min.BedGraph
sed -i 's/^chr//' ${BEDPATH}/${id}_plu.BedGraph

Subsequently, the BedGraph files were successfully reformatted to the format:

1    14764    14914    1
1    138450    138599    1
1    353918    354067    1
1    361855    362005    1
1    364138    364288    1
1    564602    564603    1

Please ensure to delete any previously generated empty temporary files before running the commands.