syntaxerror while running permutation_peakcaller

[parhampey]

Hey I am trying to call peaks with the permutation_callpeak subcommand but am getting the following error. Any idea what is going on?

Traceback (most recent call last):
File "/Users/parhampeyda/opt/anaconda3/bin/CLAM", line 4, in
import('pkg_resources').run_script('CLAM==1.2.0', 'CLAM')
File "/Users/parhampeyda/opt/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 "/Users/parhampeyda/opt/anaconda3/lib/python3.8/site-packages/pkg_resources/init.py", line 1455, in run_script
exec(script_code, namespace, namespace)
File "/Users/parhampeyda/opt/anaconda3/lib/python3.8/site-packages/CLAM-1.2.0-py3.8.egg/EGG-INFO/scripts/CLAM", line 326, in
File "/Users/parhampeyda/opt/anaconda3/lib/python3.8/site-packages/CLAM-1.2.0-py3.8.egg/EGG-INFO/scripts/CLAM", line 69, in main
File "", line 991, in _find_and_load
File "", line 971, in _find_and_load_unlocked
File "", line 914, in _find_spec
File "", line 1342, in find_spec
File "", line 1316, in _get_spec
File "", line 1297, in _legacy_get_spec
File "", line 414, in spec_from_loader
File "", line 649, in spec_from_file_location
File "", line 191, in get_filename
File "", line 713, in _get_module_code
File "", line 647, in _compile_source
File "/Users/parhampeyda/opt/anaconda3/lib/python3.8/site-packages/CLAM-1.2.0-py3.8.egg/CLAM/permutation_peakcaller.py", line 157
(unibam_file, multibam_file, child_gene_list, gene_annot,
^
SyntaxError: invalid syntax

[parhampey]

Looks like this was because I was running the software with Python 3. When I switched to Python 2 I don't get this error anymore. However, I am getting another error

File "build/bdist.macosx-10.6-x86_64/egg/CLAM/permutation_peakcaller.py", line 62, in parser
IndexError: list index out of range

Not sure what is going on now.

[wkdeng]

Thanks for point it out. Previously, we require both multi-mapped reads and uniquely mapped reads (generated by preprocessor), now only 1 input bam is allowed.