{"action":"created","issue":{"url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/4","repository_url":"https://api.github.com/repos/knights-lab/SHOGUN","labels_url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/4/comments","events_url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/4/events","html_url":"https://github.com/knights-lab/SHOGUN/issues/4","id":201378645,"number":4,"title":"last_common_ancestor.py import module find_betweens error","user":{"login":"qiyunzhu","id":4396343,"avatar_url":"https://avatars.githubusercontent.com/u/4396343?v=3","gravatar_id":"","url":"https://api.github.com/users/qiyunzhu","html_url":"https://github.com/qiyunzhu","followers_url":"https://api.github.com/users/qiyunzhu/followers","following_url":"https://api.github.com/users/qiyunzhu/following{/other_user}","gists_url":"https://api.github.com/users/qiyunzhu/gists{/gist_id}","starred_url":"https://api.github.com/users/qiyunzhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiyunzhu/subscriptions","organizations_url":"https://api.github.com/users/qiyunzhu/orgs","repos_url":"https://api.github.com/users/qiyunzhu/repos","events_url":"https://api.github.com/users/qiyunzhu/events{/privacy}","received_events_url":"https://api.github.com/users/qiyunzhu/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2017-01-17T19:14:32Z","updated_at":"2017-01-18T18:49:51Z","closed_at":null,"body":"This error occurs when I followed the README.md to run with the example dataset. The full screen output is:\r\n```\r\n(shogun) -bash-4.1$ shogun_bt2_lca -i ./mock_communities -b ./annotated/bt2/test.hmp_species\r\nTraceback (most recent call last):\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/bin/shogun_bt2_lca\", line 11, in <module>\r\n    load_entry_point('shogun==0.0.1.dev0', 'console_scripts', 'shogun_bt2_lca')()\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 561, in load_entry_point\r\n    return get_distribution(dist).load_entry_point(group, name)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2631, in load_entry_point\r\n    return ep.load()\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2291, in load\r\n    return self.resolve()\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/pkg_resources/__init__.py\", line 2297, in resolve\r\n    module = __import__(self.module_name, fromlist=['__name__'], level=0)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/shogun/scripts/shogun_bt2_lca.py\", line 7, in <module>\r\n    from shogun.utils.last_common_ancestor import build_lca_map\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/shogun/utils/__init__.py\", line 1, in <module>\r\n    from .last_common_ancestor import build_lca_map\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/shogun/utils/last_common_ancestor.py\", line 1, in <module>\r\n    from find_betweens import verify_make_dir\r\nModuleNotFoundError: No module named 'find_betweens'\r\n```\r\nThe computer system is:\r\n```\r\n(shogun) -bash-4.1$ uname -a\r\nLinux some.addr.edu 2.6.32-504.23.4.el6.x86_64 #1 SMP Tue Jun 9 20:57:37 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux\r\n```\r\nThank you!"},"comment":{"url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/comments/273564759","html_url":"https://github.com/knights-lab/SHOGUN/issues/4#issuecomment-273564759","issue_url":"https://api.github.com/repos/knights-lab/SHOGUN/issues/4","id":273564759,"user":{"login":"qiyunzhu","id":4396343,"avatar_url":"https://avatars.githubusercontent.com/u/4396343?v=3","gravatar_id":"","url":"https://api.github.com/users/qiyunzhu","html_url":"https://github.com/qiyunzhu","followers_url":"https://api.github.com/users/qiyunzhu/followers","following_url":"https://api.github.com/users/qiyunzhu/following{/other_user}","gists_url":"https://api.github.com/users/qiyunzhu/gists{/gist_id}","starred_url":"https://api.github.com/users/qiyunzhu/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/qiyunzhu/subscriptions","organizations_url":"https://api.github.com/users/qiyunzhu/orgs","repos_url":"https://api.github.com/users/qiyunzhu/repos","events_url":"https://api.github.com/users/qiyunzhu/events{/privacy}","received_events_url":"https://api.github.com/users/qiyunzhu/received_events","type":"User","site_admin":false},"created_at":"2017-01-18T18:49:51Z","updated_at":"2017-01-18T18:49:51Z","body":"Hi @bhillmann I installed the update and now the problem is gone! Thanks!\r\n```\r\nI also tried the UTree option, but here is the error message:\r\n(shogun) -bash-4.1$ shogun_utree_db -i ./test.hmp_species.fna -x '>, '\r\nTraceback (most recent call last):\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/bin/shogun_utree_db\", line 11, in <module>\r\n    load_entry_point('shogun==0.0.1.dev0', 'console_scripts', 'shogun_utree_db')()\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/click/core.py\", line 722, in __call__\r\n    return self.main(*args, **kwargs)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/click/core.py\", line 697, in main\r\n    rv = self.invoke(ctx)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/click/core.py\", line 895, in invoke\r\n    return ctx.invoke(self.callback, **ctx.params)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/click/core.py\", line 535, in invoke\r\n    return callback(*args, **kwargs)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/shogun/scripts/shogun_utree_db.py\", line 71, in shogun_utree_db\r\n    print(utree_build(outf_fasta, outf_map, path_uncompressed_tree, threads=threads))\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/shogun/wrappers/utree.py\", line 15, in utree_build\r\n    return run_command(cmd, shell=shell)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/site-packages/ninja_utils/utils/run_command.py\", line 20, in run_command\r\n    cwd=os.getcwd(),\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/subprocess.py\", line 336, in check_output\r\n    **kwargs).stdout\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/subprocess.py\", line 403, in run\r\n    with Popen(*popenargs, **kwargs) as process:\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/subprocess.py\", line 707, in __init__\r\n    restore_signals, start_new_session)\r\n  File \"/home/me/Programs/Miniconda2/envs/shogun/lib/python3.6/subprocess.py\", line 1326, in _execute_child\r\n    raise child_exception_type(errno_num, err_msg)\r\nFileNotFoundError: [Errno 2] No such file or directory: 'utree-build'\r\n```"}}
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