error when running oncodrivefml

Issue #23 new
Former user created an issue

oncodrivefml -t noncoding -i 1205mydata.overlap-5col.txt -e 02_3utr.regions.gz -s wgs --output mydata-3utr 2019-12-14 13:58:27 oncodrivefml INFO -- Using HG19 as reference genome 2019-12-14 13:58:27 oncodrivefml INFO -- Running analysis 2019-12-14 13:58:27 oncodrivefml INFO -- Building regions tree Traceback (most recent call last): File "/miniconda2/bin/oncodrivefml", line 11, in <module> sys.exit(cmdline()) File "/miniconda2/lib/python3.6/site-packages/click/core.py", line 764, in call return self.main(args, kwargs) File "/miniconda2/lib/python3.6/site-packages/click/core.py", line 717, in main rv = self.invoke(ctx) File "/miniconda2/lib/python3.6/site-packages/click/core.py", line 956, in invoke return ctx.invoke(self.callback, ctx.params) File "/miniconda2/lib/python3.6/site-packages/click/core.py", line 555, in invoke return callback(args, **kwargs) File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/main.py", line 104, in cmdline override_config) File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/main.py", line 56, in main analysis.run() File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/oncodrivefml.py", line 189, in run save_pickle=self.generate_pickle) File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/load.py", line 230, in load_and_map_variants elements_tree = load_elements_tree(elements_file) File "/miniconda2/lib/python3.6/site-packages/bgcache/decorator.py", line 81, in new_function cached_value = old_function(input_file) File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/load.py", line 181, in load_elements_tree return build_regions_tree(elements) File "/miniconda2/lib/python3.6/site-packages/oncodrivefml/load.py", line 164, in build_regions_tree for i, (k, allr) in enumerate(regions.items()): AttributeError: 'generator' object has no attribute 'items'

Comments (2)

  1. Log in to comment