mnshgl0110
commented
1 year ago Were you able to run the example pipeline?
Closed emmannaemeka closed 7 months ago
mnshgl0110
commented
1 year ago Were you able to run the example pipeline?
Hi, I am trying to run syri with the following command and got the error message below. What can be the problem?
syri -c out.filtered.coords -d out.filtered.delta -r cbs138.fasta -q a9_scaffold.qry.fasta Traceback (most recent call last): File "/Users/emmannaemeka/mambaforge/bin/syri", line 4, in
import('pkg_resources').run_script('syri==1.6.4', 'syri')
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/pkg_resources/init.py", line 672, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/pkg_resources/init.py", line 1472, in run_script
exec(code, namespace, namespace)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/syri-1.6.4-py3.9-macosx-10.9-x86_64.egg/EGG-INFO/scripts/syri", line 6, in
main(sys.argv[1:])
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/syri-1.6.4-py3.9-macosx-10.9-x86_64.egg/syri/scripts/syri.py", line 326, in main
syri(args)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/site-packages/syri-1.6.4-py3.9-macosx-10.9-x86_64.egg/syri/scripts/syri.py", line 213, in syri
startSyri(args, coords[["aStart", "aEnd", "bStart", "bEnd", "aLen", "bLen", "iden", "aDir", "bDir", "aChr", "bChr"]])
File "syri/pyxFiles/synsearchFunctions.pyx", line 508, in syri.synsearchFunctions.startSyri
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/context.py", line 119, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild,
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/pool.py", line 212, in init
self._repopulate_pool()
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/pool.py", line 303, in _repopulate_pool
return self._repopulate_pool_static(self._ctx, self.Process,
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/pool.py", line 326, in _repopulate_pool_static
w.start()
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/process.py", line 121, in start
self._popen = self._Popen(self)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/context.py", line 284, in _Popen
return Popen(process_obj)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 32, in init
super().init(process_obj)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/popen_fork.py", line 19, in init
self._launch(process_obj)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/popen_spawn_posix.py", line 42, in _launch
prep_data = spawn.get_preparation_data(process_obj._name)
File "/Users/emmannaemeka/mambaforge/lib/python3.9/multiprocessing/spawn.py", line 183, in get_preparation_data
main_mod_name = getattr(main_module.spec, "name", None)
AttributeError: module 'main' has no attribute 'spec'