{"action":"created","issue":{"url":"https://api.github.com/repos/ijuric/MAPS/issues/2","repository_url":"https://api.github.com/repos/ijuric/MAPS","labels_url":"https://api.github.com/repos/ijuric/MAPS/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/ijuric/MAPS/issues/2/comments","events_url":"https://api.github.com/repos/ijuric/MAPS/issues/2/events","html_url":"https://github.com/ijuric/MAPS/issues/2","id":385772977,"node_id":"MDU6SXNzdWUzODU3NzI5Nzc=","number":2,"title":"String index out of range error","user":{"login":"mapsuser1","id":45461140,"node_id":"MDQ6VXNlcjQ1NDYxMTQw","avatar_url":"https://avatars1.githubusercontent.com/u/45461140?v=4","gravatar_id":"","url":"https://api.github.com/users/mapsuser1","html_url":"https://github.com/mapsuser1","followers_url":"https://api.github.com/users/mapsuser1/followers","following_url":"https://api.github.com/users/mapsuser1/following{/other_user}","gists_url":"https://api.github.com/users/mapsuser1/gists{/gist_id}","starred_url":"https://api.github.com/users/mapsuser1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mapsuser1/subscriptions","organizations_url":"https://api.github.com/users/mapsuser1/orgs","repos_url":"https://api.github.com/users/mapsuser1/repos","events_url":"https://api.github.com/users/mapsuser1/events{/privacy}","received_events_url":"https://api.github.com/users/mapsuser1/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2018-11-29T14:52:32Z","updated_at":"2018-11-30T23:30:13Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nBelow is an error log that I keep getting (some paths redacted). It seems to refer to an index out of range. Do you have any advice on what could be causing this issue?\r\n\r\n\r\nTraceback (most recent call last):\r\n  File \"/X/MAPS/bin/feather/feather_pipe\", line 116, in <module>\r\n    main()\r\n  File \"/X/MAPS/bin/feather/feather_pipe\", line 50, in main\r\n    split_main(filter_output_filename, outdir, prefix, length_threshold, per_chr_bedpe, generate_hic)\r\n  File \"/X/MAPS/bin/feather/feather_split_rongxin.py\", line 25, in split_main\r\n    autosomal_chrs = [chr_name for chr_name in chr_list if (chr_name.find('_') == -1 and chr_name[3].isdigit())]\r\n  File \"/X/MAPS/bin/feather/feather_split_rongxin.py\", line 25, in <listcomp>\r\n    autosomal_chrs = [chr_name for chr_name in chr_list if (chr_name.find('_') == -1 and chr_name[3].isdigit())]\r\n**IndexError: string index out of range**\r\nusage: PROG [-h] [--BINNING_RANGE BINNING_RANGE]\r\n            DATASET_NAME OUT_DIR MACS2_PATH GF_PATH LONG_PATH SHORT_PATH\r\n            BIN_SIZE N_CHROMS OUT_FILE_PATH\r\nPROG: error: the following arguments are required: OUT_FILE_PATH\r\nTraceback (most recent call last):\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 225, in <module>\r\n    main()\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 222, in main\r\n    init(p)\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 78, in init\r\n    input_data = pd.read_csv(p.run_file,sep='=',skip_blank_lines=True, comment='#',index_col=0,header=None)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 709, in parser_f\r\n    return _read(filepath_or_buffer, kwds)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 449, in _read\r\n    parser = TextFileReader(filepath_or_buffer, **kwds)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 818, in __init__\r\n    self._make_engine(self.engine)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 1049, in _make_engine\r\n    self._engine = CParserWrapper(self.f, **self.options)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 1695, in __init__\r\n    self._reader = parsers.TextReader(src, **kwds)\r\n  File \"pandas/_libs/parsers.pyx\", line 402, in pandas._libs.parsers.TextReader.__cinit__\r\n  File \"pandas/_libs/parsers.pyx\", line 718, in pandas._libs.parsers.TextReader._setup_parser_source\r\nFileNotFoundError: File b'/X/MAPS_output/sra_data_20181128_193810/maps_sra_data.maps' does not exist\r\nLoading required package: methods\r\nLoading required package: stats4\r\nLoading required package: splines\r\nError in file(file, \"rt\") : cannot open the connection\r\nCalls: read.table -> file\r\nExecution halted\r\nError in file(file, \"rt\") : cannot open the connection\r\nCalls: read.table -> file\r\nIn addition: Warning message:\r\nIn file(file, \"rt\") :\r\n  cannot open file '/X/MAPS_output/sra_data_20181128_193810/sra_data.5k.2.peaks': No such file or directory\r\nExecution halted\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/ijuric/MAPS/issues/comments/443371125","html_url":"https://github.com/ijuric/MAPS/issues/2#issuecomment-443371125","issue_url":"https://api.github.com/repos/ijuric/MAPS/issues/2","id":443371125,"node_id":"MDEyOklzc3VlQ29tbWVudDQ0MzM3MTEyNQ==","user":{"login":"mapsuser1","id":45461140,"node_id":"MDQ6VXNlcjQ1NDYxMTQw","avatar_url":"https://avatars1.githubusercontent.com/u/45461140?v=4","gravatar_id":"","url":"https://api.github.com/users/mapsuser1","html_url":"https://github.com/mapsuser1","followers_url":"https://api.github.com/users/mapsuser1/followers","following_url":"https://api.github.com/users/mapsuser1/following{/other_user}","gists_url":"https://api.github.com/users/mapsuser1/gists{/gist_id}","starred_url":"https://api.github.com/users/mapsuser1/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mapsuser1/subscriptions","organizations_url":"https://api.github.com/users/mapsuser1/orgs","repos_url":"https://api.github.com/users/mapsuser1/repos","events_url":"https://api.github.com/users/mapsuser1/events{/privacy}","received_events_url":"https://api.github.com/users/mapsuser1/received_events","type":"User","site_admin":false},"created_at":"2018-11-30T23:30:13Z","updated_at":"2018-11-30T23:30:13Z","author_association":"NONE","body":"I switched to the GRCh38 reference recommended in the MAPS documentation, and the index out of range issue seems to be avoided. However, MAPS fails afterwards with the following error log:\r\n\r\nusage: PROG [-h] [--BINNING_RANGE BINNING_RANGE]\r\n            DATASET_NAME OUT_DIR MACS2_PATH GF_PATH LONG_PATH SHORT_PATH\r\n            BIN_SIZE N_CHROMS OUT_FILE_PATH\r\nPROG: error: the following arguments are required: OUT_FILE_PATH\r\nTraceback (most recent call last):\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 225, in <module>\r\n    main()\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 222, in main\r\n    init(p)\r\n  File \"/X/MAPS/bin/MAPS/MAPS.py\", line 78, in init\r\n    input_data = pd.read_csv(p.run_file,sep='=',skip_blank_lines=True, comment='#',index_col=0,header=None)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 709, in parser_f\r\n    return _read(filepath_or_buffer, kwds)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 449, in _read\r\n    parser = TextFileReader(filepath_or_buffer, **kwds)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 818, in __init__\r\n    self._make_engine(self.engine)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 1049, in _make_engine\r\n    self._engine = CParserWrapper(self.f, **self.options)\r\n  File \"/X/.local/lib/python3.4/site-packages/pandas/io/parsers.py\", line 1695, in __init__\r\n    self._reader = parsers.TextReader(src, **kwds)\r\n  File \"pandas/_libs/parsers.pyx\", line 402, in pandas._libs.parsers.TextReader.__cinit__\r\n  File \"pandas/_libs/parsers.pyx\", line 718, in pandas._libs.parsers.TextReader._setup_parser_source\r\nFileNotFoundError: File b'/X/MAPS_output/sra_data_20181130_092609/maps_sra_data.maps' does not exist\r\nLoading required package: methods\r\nLoading required package: stats4\r\nLoading required package: splines\r\nError in file(file, \"rt\") : cannot open the connection\r\nCalls: read.table -> file\r\nExecution halted\r\nError in file(file, \"rt\") : cannot open the connection\r\nCalls: read.table -> file\r\nIn addition: Warning message:\r\nIn file(file, \"rt\") :\r\n  cannot open file 'X/MAPS_output/sra_data_20181130_092609/sra_data.5k.2.peaks': No such file or directory\r\nExecution halted\r\n\r\n Let me know if you have any advice on this error.\r\n"}}
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