{"action":"closed","issue":{"url":"https://api.github.com/repos/niemasd/FAVITES/issues/6","repository_url":"https://api.github.com/repos/niemasd/FAVITES","labels_url":"https://api.github.com/repos/niemasd/FAVITES/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/niemasd/FAVITES/issues/6/comments","events_url":"https://api.github.com/repos/niemasd/FAVITES/issues/6/events","html_url":"https://github.com/niemasd/FAVITES/issues/6","id":304834433,"number":6,"title":"running error on Calab ","user":{"login":"smazrouee","id":5768208,"avatar_url":"https://avatars3.githubusercontent.com/u/5768208?v=4","gravatar_id":"","url":"https://api.github.com/users/smazrouee","html_url":"https://github.com/smazrouee","followers_url":"https://api.github.com/users/smazrouee/followers","following_url":"https://api.github.com/users/smazrouee/following{/other_user}","gists_url":"https://api.github.com/users/smazrouee/gists{/gist_id}","starred_url":"https://api.github.com/users/smazrouee/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/smazrouee/subscriptions","organizations_url":"https://api.github.com/users/smazrouee/orgs","repos_url":"https://api.github.com/users/smazrouee/repos","events_url":"https://api.github.com/users/smazrouee/events{/privacy}","received_events_url":"https://api.github.com/users/smazrouee/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-03-13T16:16:35Z","updated_at":"2018-03-13T23:58:31Z","closed_at":"2018-03-13T23:58:31Z","author_association":"NONE","body":"<!--- Provide a general summary of the issue in the Title above -->\r\nSounds like problem with docker deamon or sth\r\n## FAVITES Version\r\n<!--- Provide the FAVITES version number you used. If there is a later version, please first try that to see if the issue has been fixed -->\r\n\r\n## Environment\r\n<!--- What OS, and how are you running FAVITES (e.g. Docker)? -->\r\n\r\n## Configuration File\r\n<!--- Include your configuration file here -->\r\n{\r\n\"ContactNetwork\": \"NetworkX\",\r\n\"ContactNetworkGenerator\": \"RandomPartitionGraph\",\r\n\"d_or_u\": \"u\",\r\n\r\n\"rpg_p_in\": 0.004,\r\n\"rpg_p_out\": 0.0002,\r\n\"rpg_sizes\": [1000,1000,1000,1000,1000],\r\n\"end_time\": 10,\r\n\"num_seeds\": 50,\r\n\"out_dir\": \"/Users/sepideh/FAVITES/output/set1/output_1_1\",\r\n\r\n\"Driver\": \"Default\",\r\n\"EndCriteria\": \"GEMF\",\r\n\"Logging\": \"File\",\r\n\r\n\"NodeAvailability\": \"Bernoulli\",\r\n\"node_sample_prob\": 0.1,\r\n\"NumBranchSample\": \"Single\",\r\n\"NumTimeSample\": \"Once\",\r\n\"SourceSample\": \"Random\",\r\n\"TimeSample\": \"GranichFirstART\",\r\n\r\n\"NodeEvolution\": \"VirusTreeSimulator\",\r\n\"vts_growthRate\": 2.851904,\r\n\"vts_model\": \"logistic\",\r\n\"vts_n0\": 1,\r\n\"vts_t50\": -2,\r\n\r\n\"PostValidation\": \"Dummy\",\r\n\r\n\"SeedSelection\": \"Random\",\r\n\r\n\"SeedSequence\": \"VirusPureCoalescentGTRGamma\",\r\n\"viral_sequence_type\": \"HIV1-B-DNA-POL-LITTLE\",\r\n\r\n\"SequenceEvolution\": \"GTRGammaSeqGen\",\r\n\"Sequencing\": \"Perfect\",\r\n\r\n\"TransmissionNodeSample\": \"GEMF\",\r\n\"hiv_a1_to_d\": 0,\r\n\"hiv_a2_to_a3\": 0,\r\n\"hiv_a2_to_d\": 0,\r\n\"hiv_a1_to_i1\": 0.48,\r\n\"hiv_a2_to_i2\": 0.48,\r\n\"hiv_i2_to_a2\": 0.5,\r\n\"hiv_i1_to_a1\": 0.5,\r\n\"hiv_a3_to_a4\": 0,\r\n\"hiv_a3_to_d\": 0,\r\n\"hiv_a3_to_i3\": 0,\r\n\"hiv_a4_to_d\": 0,\r\n\"hiv_a4_to_i4\": 0,\r\n\"hiv_i1_to_d\": 0,\r\n\"hiv_i1_to_i2\": 8.666666666666666,\r\n\"hiv_a1_to_a2\": 4.33333,\r\n\"hiv_i2_to_d\": 0,\r\n\"hiv_i2_to_i3\": 0,\r\n\"hiv_i3_to_a3\": 0,\r\n\"hiv_i3_to_d\": 0,\r\n\"hiv_i3_to_i4\": 0,\r\n\"hiv_i4_to_a4\": 0,\r\n\"hiv_i4_to_d\": 0,\r\n\"hiv_ns_to_d\": 0,\r\n\"hiv_ns_to_s\": 999999,\r\n\"hiv_s_to_d\": 0,\r\n\"hiv_s_to_i1_by_a1\": 0.005625,\r\n\"hiv_s_to_i1_by_a2\": 0,\r\n\"hiv_s_to_i1_by_a3\": 0,\r\n\"hiv_s_to_i1_by_a4\": 0,\r\n\"hiv_s_to_i1_by_i1\": 0.1125,\r\n\"hiv_s_to_i1_by_i2\": 0.1,\r\n\"hiv_s_to_i1_by_i3\": 0,\r\n\"hiv_s_to_i1_by_i4\": 0,\r\n\"hiv_s_to_i1_seed\": 0,\r\n\"TransmissionTimeSample\": \"HIVARTGranichGEMF\",\r\n\r\n\r\n\"TreeNode\": \"Simple\",\r\n\"TreeUnit\": \"LogNormal\",\r\n\"tree_rate_mean\": -6.164,\r\n\"tree_rate_stdev\": 0.3,\r\n\r\n\"grinder_path\": \"grinder\",\r\n\"gemf_path\": \"GEMF\",\r\n\"hmmemit_path\": \"hmmemit\",\r\n\"java_path\": \"java\",\r\n\"nw_rename_path\": \"nw_rename\",\r\n\"seqgen_path\": \"seq-gen\",\r\n\r\n\"seed_population\": 20,\r\n\r\n\"seqgen_a_to_c\": 1.765707,\r\n\"seqgen_a_to_g\": 9.587649,\r\n\"seqgen_a_to_t\": 0.691915,\r\n\"seqgen_c_to_g\": 0.863348,\r\n\"seqgen_c_to_t\": 10.282617,\r\n\"seqgen_freq_a\": 0.392,\r\n\"seqgen_freq_c\": 0.165,\r\n\"seqgen_freq_g\": 0.212,\r\n\"seqgen_freq_t\": 0.232,\r\n\"seqgen_g_to_t\": 1.0,\r\n\"seqgen_gamma_shape\": 0.405129,\r\n\"seqgen_num_gamma_rate_categories\": \"\"\r\n\r\n}\r\n\r\n## Unexpected Behavior\r\n<!--- What happened, and how did it deviate from what you were expecting? Include the full error message if applicable -->\r\nrun_favites_docker.py -c CONFIG1-1.json \r\nGot permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Get http://%2Fvar%2Frun%2Fdocker.sock/v1.35/images/json: dial unix /var/run/docker.sock: connect: permission denied\r\nTraceback (most recent call last):\r\n  File \"/calab_data/mirarab/home//sepideh/.bin/run_favites_docker.py\", line 31, in <module>\r\n    o = check_output(['docker','images']).decode().splitlines()\r\n  File \"/usr/lib/python3.4/subprocess.py\", line 620, in check_output\r\n    raise CalledProcessError(retcode, process.args, output=output)\r\nsubprocess.CalledProcessError: Command '['docker', 'images']' returned non-zero exit status 1\r\n\r\nDuring handling of the above exception, another exception occurred:\r\n\r\nTraceback (most recent call last):\r\n  File \"/calab_data/mirarab/home//sepideh/.bin/run_favites_docker.py\", line 36, in <module>\r\n    raise RuntimeError(\"docker images command failed\\n%s\"%e.output)\r\nRuntimeError: docker images command failed\r\nb''\r\n"}}
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