{"action":"created","issue":{"url":"https://api.github.com/repos/haotianteng/Chiron/issues/64","repository_url":"https://api.github.com/repos/haotianteng/Chiron","labels_url":"https://api.github.com/repos/haotianteng/Chiron/issues/64/labels{/name}","comments_url":"https://api.github.com/repos/haotianteng/Chiron/issues/64/comments","events_url":"https://api.github.com/repos/haotianteng/Chiron/issues/64/events","html_url":"https://github.com/haotianteng/Chiron/issues/64","id":342199534,"node_id":"MDU6SXNzdWUzNDIxOTk1MzQ=","number":64,"title":"appear at different stage: AttributeError: 'tqdm' object has no attribute 'pos' ","user":{"login":"Huanle","id":909201,"node_id":"MDQ6VXNlcjkwOTIwMQ==","avatar_url":"https://avatars3.githubusercontent.com/u/909201?v=4","gravatar_id":"","url":"https://api.github.com/users/Huanle","html_url":"https://github.com/Huanle","followers_url":"https://api.github.com/users/Huanle/followers","following_url":"https://api.github.com/users/Huanle/following{/other_user}","gists_url":"https://api.github.com/users/Huanle/gists{/gist_id}","starred_url":"https://api.github.com/users/Huanle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Huanle/subscriptions","organizations_url":"https://api.github.com/users/Huanle/orgs","repos_url":"https://api.github.com/users/Huanle/repos","events_url":"https://api.github.com/users/Huanle/events{/privacy}","received_events_url":"https://api.github.com/users/Huanle/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-07-18T06:55:15Z","updated_at":"2018-07-24T13:03:44Z","closed_at":null,"author_association":"NONE","body":"Hi Haotian,\r\n\r\nI ran into the following error and it seems to pop up at different time during multiple trials of \r\n\r\n```\r\n$ chiron call -i 736688-175.fast5/ -o ./ -m ~/h.liu/scripts/chiron/chiron/model/DNA_default/ -b 4  -t 6\r\n\r\n/home/913/hl0222/.local/lib/python2.7/site-packages/h5py/__init__.py:34: FutureWarning: Conversion of the second argument of issubdtype from `float` to `np.floating` is deprecated. In future, it will be treated as `np.float64 == np.dtype(float).type`.\r\n  from ._conv import register_converters as _register_converters\r\nSubdirectory processing:: 1it [01:04, 64.80s/it]\r\n2018-07-18 16:32:16.327732: I tensorflow/core/platform/cpu_feature_guard.cc:137] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA\r\n2018-07-18 16:32:16.563024: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1030] Found device 0 with properties:\r\nname: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235\r\npciBusID: 0000:84:00.0\r\ntotalMemory: 11.17GiB freeMemory: 11.10GiB\r\n2018-07-18 16:32:16.731698: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1030] Found device 1 with properties:\r\nname: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235\r\npciBusID: 0000:85:00.0\r\ntotalMemory: 11.17GiB freeMemory: 11.10GiB\r\n2018-07-18 16:32:16.732188: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1045] Device peer to peer matrix\r\n2018-07-18 16:32:16.732255: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1051] DMA: 0 1\r\n2018-07-18 16:32:16.732287: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1061] 0:   Y Y\r\n2018-07-18 16:32:16.732309: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1061] 1:   Y Y\r\n2018-07-18 16:32:16.732338: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:0) -> (device: 0, name: Tesla K80, pci bus id: 0000:84:00.0, compute capability: 3.7)\r\n2018-07-18 16:32:16.732363: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1120] Creating TensorFlow device (/device:GPU:1) -> (device: 1, name: Tesla K80, pci bus id: 0000:85:00.0, compute capability: 3.7)\r\nLogits inferencing.:   0%|          | 4/3996 [05:31<91:56:43, 82.92s/it]                  Exception\r\nLogits inferencing:   0%|          | 0/83 [00:00<?, ?it/s] in <bound method tqdm.__del__ of CTC decoding.:   0%|          | 3/3996 [05:31<122:37:42, 110.56s/it]> ignored7, 27.79s/it]Traceback (most recent call last):\r\n  File \"/home/913/hl0222/.local/bin/chiron\", line 11, in <module>]decoded_q=0, logits_q=0]\r\n    load_entry_point('chiron==0.4', 'console_scripts', 'chiron')()\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/chiron/entry.py\", line 91, in main\r\n    args.func(args)\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/chiron/entry.py\", line 26, in evaluation\r\n    chiron_eval.run(args)\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/chiron/chiron_eval.py\", line 398, in run\r\n    time_dict = unix_time(evaluation)\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/chiron/utils/unix_time.py\", line 21, in unix_time\r\n    function(*args, **kwargs)\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/chiron/chiron_eval.py\", line 307, in evaluation\r\n    break\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/tqdm-4.23.4-py2.7.egg/tqdm/_tqdm.py\", line 878, in __exit__\r\n    self.close()\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/tqdm-4.23.4-py2.7.egg/tqdm/_tqdm.py\", line 1087, in close\r\n    self._decr_instances(self)\r\n  File \"/home/913/hl0222/.local/lib/python2.7/site-packages/tqdm-4.23.4-py2.7.egg/tqdm/_tqdm.py\", line 446, in _decr_instances\r\n    if inst.pos > abs(instance.pos):\r\nAttributeError: 'tqdm' object has no attribute 'pos'\r\n```\r\n\r\nAlthough it seems to be tqdm specific issue. I have no clue to fix it.\r\nHope you can help me sort it out.\r\n\r\nThanks a lot.\r\n\r\nHuanlee"},"comment":{"url":"https://api.github.com/repos/haotianteng/Chiron/issues/comments/407398804","html_url":"https://github.com/haotianteng/Chiron/issues/64#issuecomment-407398804","issue_url":"https://api.github.com/repos/haotianteng/Chiron/issues/64","id":407398804,"node_id":"MDEyOklzc3VlQ29tbWVudDQwNzM5ODgwNA==","user":{"login":"Huanle","id":909201,"node_id":"MDQ6VXNlcjkwOTIwMQ==","avatar_url":"https://avatars3.githubusercontent.com/u/909201?v=4","gravatar_id":"","url":"https://api.github.com/users/Huanle","html_url":"https://github.com/Huanle","followers_url":"https://api.github.com/users/Huanle/followers","following_url":"https://api.github.com/users/Huanle/following{/other_user}","gists_url":"https://api.github.com/users/Huanle/gists{/gist_id}","starred_url":"https://api.github.com/users/Huanle/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Huanle/subscriptions","organizations_url":"https://api.github.com/users/Huanle/orgs","repos_url":"https://api.github.com/users/Huanle/repos","events_url":"https://api.github.com/users/Huanle/events{/privacy}","received_events_url":"https://api.github.com/users/Huanle/received_events","type":"User","site_admin":false},"created_at":"2018-07-24T13:03:44Z","updated_at":"2018-07-24T13:03:44Z","author_association":"NONE","body":"@haotianteng \r\n\r\nthere are 3996 *signal files in raw/ folder.\r\nlast file in result/ folder corresponds to the 3029th file in /raw folder. \r\nSo it seems bascalling is done though it is unbelievable that only 27 reads were basecalled.\r\nI will double check it. But still the error message is confusing."}}
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