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DataAnalysisWrapperErrors.py
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import sys, os
class DataAnalysisWrapperError(Exception):
pass
class UnknownOSError(Exception):
em = {1001: 'Unknown operating system. Please run on Windows, Mac OSX, or Linux. Exiting...'}
class OptionError(Exception):
em = {1101: 'Unknown option. See above for usage details. Exiting...',
1102: 'Missing --input_dir (-i) option. See above for usage details. Exiting...',
1103: 'input_dir is incorrectly specified. Needs to end in "' + os.path.join('...','<runid>','Data','Intensities','BaseCalls','') + '". Exiting...',
1104: 'Run ID inferred from input_dir is not of the correct format. Exiting...',
1105: 'Missing --config_file (-c) option. See above for usage details. Exiting...'}
class PathError(Exception):
em = {1201: 'Path specified by --pipeline_path (-p) does not exist. Exiting...',
1202: 'Path specified by --basecalls_dir (-i) does not exist. Exiting...',
1203: 'Path specified by --results_dir (-u) does not exist. Exiting...',
1204: 'Path specified by --outfiles_dir (-a) does not exist. Exiting...',
1205: 'Path specified by --cache_dir (-z) does not exist. Exiting...',
1206: 'Path specified by --raw_outfile (-w) does not exist. Exiting...',
1207: 'Path specified by --csv_outfile (-o) does not exist. Exiting...',
1208: 'Path specified by --db_outfile (-d) does not exist. Exiting...',
1209: 'Path specified by --stats_outfile (-t) does not exist. Exiting...',
1210: 'Path specified by --ss_outfile (-v) does not exist. Exiting...',
1211: 'Path specified by --csv_cache (-c) does not exist. Exiting...',
1212: 'Path specified by --sample_sheet (-s) does not exist. Exiting...',
1213: 'SampleSheet.csv not found in root run folder. Exiting...',
1214: 'Run specific directory within specified working directory already exists. Use --force to overwrite. Exiting...'}
class SSValidatorError(Exception):
em = {1301: 'There are multiple rows with "[Data]" in first column (should be only one). Exiting...',
1302: 'There are no rows with "[Data]" in first column (should be only one). Exiting...',
1303: 'Sample sheet does not have "Sample_ID" column. Exiting...',
1304: 'Sample sheet does not have "Sample_Name" column. Exiting...',
1305: 'Sample sheet does not have "Sample_Project" column. Exiting...',
1306: 'Sample sheet does not have "Source" column. Exiting...',
1307: 'Sample sheet does not have "Input" column. Exiting...',
1308: 'Problem matching FastQ files. Exiting...',
1309: 'Sample sheet Sample_ID is out of order (needs to be sequential integers). Exiting...',
1310: 'Exactly 3 replicates not found for all samples labeled as "Standard". At least one standard level was not run in triplicate. Exiting...',
1311: 'At least one sample does not have a valid associated standard curve for the Assay/Source/Input/Standard_Group combination. Exiting...',
1312: 'Sample sheet does not have "Standard_Group" column. Exiting...',
1313: 'Sample sheet does not have "Batch" column. Exiting...',
1314: 'Sample sheet does not have "Checkout_Number" column. Exiting...',
1315: 'Sample sheet does not have "Ng_Per_Rxn" column. Exiting...',
1316: 'Sample sheet does not have "Phix_Fraction" column. Exiting...',
1317: 'Sample sheet does not have "Project_Version" column. Exiting...',
1318: 'Validated sample sheet not found! Check log files for details. Exiting...',
1319: 'Not all rows have int type "Sample_ID" value. Exiting...',
1320: 'Not all rows have string type "Sample_Name" value. Exiting...',
1321: '"Sample_ID" numbering issue found. "Sample_ID" column numbering must start with "1" and continue sequentially. Possible non-sequential "Sample_ID" names found. Exiting...',
1322: 'Invalid "Sample_Name" name(s) found. Non-alphanumeric characters including spaces are invalid. Exiting...',
1323: 'Sample sheet does not have "Sample_Plate" column. Exiting...',
1324: 'Sample sheet does not have "Sample_Well" column. Exiting...',
1325: 'Not all rows have string type "Sample_Plate" value. Exiting...',
1326: 'Not all rows have string type "Sample_Well" value. Exiting...',
1327: 'Sample sheet does not have "I7_Index_ID" column. Exiting...',
1328: 'Sample sheet does not have "Index" column. Exiting...',
1329: 'Not all rows have string type "Index" value. Exiting...',
1330: 'Not all rows have string type "Sample_Project" value. Exiting...',
1331: 'Not all rows have a valid "Sample_Project" value. Unrecognized assay found. Exiting...',
1332: 'Sample sheet does not have "Description" column. Exiting...',
1333: 'Not all rows have string type "Description" value. Exiting...',
1334: 'Not all rows have string type "Source" value. Exiting...',
1335: 'Not all rows have float type "Ng_Per_Rxn" value. Exiting...',
1336: 'Not all rows have float type "Phix_Fraction" value. Exiting...',
1337: 'Not all rows have string type "Batch" value. Exiting...',
1338: 'Not all rows have int type "Checkout_Number" value. Exiting...',
1339: 'Not all rows have int type "Project_Version" value. Exiting...',
1340: 'Not all rows have float type "Input" value. Exiting...',
1341: 'Not all rows have int type "Standard_Group" value. Exiting...',
1342: 'Did not find at least 4 standard curve levels per standard group. Exiting...',
1343: 'Potential mismatch in "Standard_Group" column based on the Assay/Source/Input combinations. Exiting...',}
class PipelineError(Exception):
em = {1401: 'Error when running pipeline. Exiting...'}
class ConfigFileError(Exception):
em = {1501: 'Config file missing required fields under [global]. Exiting...'}
class SequencingQcError(Exception):
em = {1601: 'Sequencing QC failed. Exiting...',
1602: '_stats.csv file not found! Check log files for details. Exiting...'}
class ReadsProcessingError(Exception):
em = {1701: 'Reads processing error. See log files. Exiting...',
1702: '_RAWCOUNTS.csv file not found! Check log files for details. Exiting...'}
class DataAnalysisError(Exception):
em = {1801: 'Data analysis error. See log files. Exiting...',
1802: '_summary.csv file not found! Check log files for details. Exiting...',
1803: '_all_plots.pdf file not found! Check log files for details. Exiting...'}
class OutputFormatterError(Exception):
em = {1901: 'Output formatter error. See log files. Exiting...',
1902: 'Unable to format "Metric" column. Exiting...',
1903: 'Unable to remap "_summary.csv" file column names. Possible missing column in unformatted "_summary" file. Exiting...',
1904: 'Unequal number of columns in unformatted "_summary.csv" and column name remapping file. Possible missing column in unformatted "_summary" file. Exiting...',}