mcmero
commented
4 years ago Hi Keyur,
Please double check your config.ini file--it should have a section labelled [BamParameters] at the top. If not, make sure this section is present. See the default svclone_config.ini for details of which sections and parameters are required.
Cheers, Marek
Hi , I am getting following error at annotate stage.
SVclone.py annotate -cfg config.ini -i simple.txt -b tumor.bam -s test --sv_format simple
Traceback (most recent call last): File "/mnt/nasapps/development/python/anaconda3/bin/SVclone.py", line 4, in
import('pkg_resources').run_script('SVclone==0.2.1', 'SVclone.py')
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1446, in run_script
exec(code, namespace, namespace)
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/site-packages/SVclone-0.2.1-py3.7.egg/EGG-INFO/scripts/SVclone.py", line 163, in
args.func(args)
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/site-packages/SVclone-0.2.1-py3.7.egg/Sclone/SVprocess/annotate.py", line 512, in preproc_svs
max_cn = float(Config.get('BamParameters', 'max_cn'))
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/configparser.py", line 780, in get
d = self._unify_values(section, vars)
File "/mnt/nasapps/development/python/anaconda3/lib/python3.7/configparser.py", line 1146, in _unify_values
raise NoSectionError(section) from None
configparser.NoSectionError: No section: 'BamParameters'
The bam fie is already indexed and i was able to validate the bam file.
Keyur