{"action":"opened","issue":{"url":"https://api.github.com/repos/Indicator/RaptorX-SS8/issues/3","labels_url":"https://api.github.com/repos/Indicator/RaptorX-SS8/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/Indicator/RaptorX-SS8/issues/3/comments","events_url":"https://api.github.com/repos/Indicator/RaptorX-SS8/issues/3/events","html_url":"https://github.com/Indicator/RaptorX-SS8/issues/3","id":110253917,"number":3,"title":"Error running run_raptorx-ss8.pl","user":{"login":"malvikasharan","id":5370471,"avatar_url":"https://avatars.githubusercontent.com/u/5370471?v=3","gravatar_id":"","url":"https://api.github.com/users/malvikasharan","html_url":"https://github.com/malvikasharan","followers_url":"https://api.github.com/users/malvikasharan/followers","following_url":"https://api.github.com/users/malvikasharan/following{/other_user}","gists_url":"https://api.github.com/users/malvikasharan/gists{/gist_id}","starred_url":"https://api.github.com/users/malvikasharan/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/malvikasharan/subscriptions","organizations_url":"https://api.github.com/users/malvikasharan/orgs","repos_url":"https://api.github.com/users/malvikasharan/repos","events_url":"https://api.github.com/users/malvikasharan/events{/privacy}","received_events_url":"https://api.github.com/users/malvikasharan/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-10-07T15:37:05Z","updated_at":"2015-10-07T15:37:05Z","closed_at":null,"body":"Hi,\r\n\r\nI am testing RaptorX at the moment. It works perfectly for 8-state secondary structure, however since it takes very long to calculate that I thought of switching to 3-state secondary structure. However, the script run_raptorx-ss3.pl fails (even for the test example given by you) showing error (Error: Unknown argument: \"d\") which I can't quite figure out.  Could you please have a look and point to the right solution?\r\n\r\nerror appears as follows:\r\nError: Unknown argument: \"d\"\r\nGenerating features...\r\n\r\nNo such file or directory at /fullpath/bin/BioDSSP.pm line 295.\r\n\r\nPredicting using CNF model...\r\n$JOB_ID 20051 5\r\n$JOB_ID bcast 20051 5\r\nparam: cnfsseight.1aaz.97375262.null cnfsseight.1aaz.97375262.input output20051\r\nnum_states: 42\r\nnum_label: 6\r\nnum_params: 12268\r\nnum_gates: 79\r\nnum_ps_gates: 21\r\nnum_pi_gates: 58\r\nwindow_size: 15\r\ndim_features: 1201\r\ndim_one_pos: 79\r\nnum_params = 12268\r\nopen model success\r\nLoading weights from /maui/malvika/rbp_prediction/seq_analysis/RnaBindEff_pipeline/APRICOT_manuscript/apricot_check/apricot_db_and_tools/raptorx/raptorx-ss3-ss8/data/3state-model.p0-1300.1342925\r\nTraining data0 loaded\r\n0 0\r\nInitialization Finished!\r\nnum_data = 0\r\nnum_tst = 0\r\n[TRAIN]begin lbfgs\r\nFormating results...\r\nDONE.\r\n"}}