Hi,
I want to use IDR to get highly repetitive peaks. For each biological repetition, we called peaks separately using SICER to get broad peaks. The output file of the software is similar to the BED file.
So, we run IDR with "--input-file-type bed". However, it failed to run successfully and the following error message is reported.
Traceback (most recent call last): File "/home/yuandy/anaconda3/bin/idr", line 4, in <module> __import__('pkg_resources').run_script('idr==2.0.3', 'idr') File "/home/yuandy/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1448, in run_script exec(code, namespace, namespace) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in <module> idr.idr.main() File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 839, in main merged_peaks, signal_type = load_samples(args) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 720, in load_samples raise ValueError("For bed files --signal-type must either "\ ValueError: For bed files --signal-type must either be set to score or an index specifying the column to use.
How should we set parameters when running with a BED file, and are there any other requirements for the BED file itself?
Looking forward to your reply!Thanks!
Hi,
I want to use IDR to get highly repetitive peaks. For each biological repetition, we called peaks separately using SICER to get broad peaks. The output file of the software is similar to the BED file.
So, we run IDR with "--input-file-type bed". However, it failed to run successfully and the following error message is reported.
Traceback (most recent call last): File "/home/yuandy/anaconda3/bin/idr", line 4, in <module> __import__('pkg_resources').run_script('idr==2.0.3', 'idr') File "/home/yuandy/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 651, in run_script self.require(requires)[0].run_script(script_name, ns) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/pkg_resources/__init__.py", line 1448, in run_script exec(code, namespace, namespace) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/EGG-INFO/scripts/idr", line 10, in <module> idr.idr.main() File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 839, in main merged_peaks, signal_type = load_samples(args) File "/home/yuandy/anaconda3/lib/python3.8/site-packages/idr-2.0.3-py3.8-linux-x86_64.egg/idr/idr.py", line 720, in load_samples raise ValueError("For bed files --signal-type must either "\ ValueError: For bed files --signal-type must either be set to score or an index specifying the column to use.How should we set parameters when running with a BED file, and are there any other requirements for the BED file itself?
Looking forward to your reply!Thanks!