Troubleshooting Errors
Input errors
number not in range of:
This error occurs when a number is entered that does not fall in the range of one or more of the following: Groups of Names, Ungrouped & Undeleted Names, and Deleted Names.
part of your input was not whitespace or numbers
This error occurs when CDSParser requests a list of numbers, and the user has inputted a character that is not a whitespace (space, tab, etc.) or that is not a digit (0, 1, etc.).
invalid integer
This error occurs when CDSparser requests a number and the input is not an integer (1,..., 10, etc.)
File errors
Corrupt file
A corrupt file error occurs when the file format is incorrect. In "defaults.def", this could be simply caused by the removal of a blank line or a variable name. Please see the example files for comparison.
File not found
A file not found error occurs when the file does not exist or is in the wrong directory. The *.def files should be in the same directory as the CDSParser.jar file.
Importing file unsuccessful
If importing your file does not acutally import any information (no names will appear in the grouping menu and outputted FASTA and tab-delimited files will contain little or no information), the file format is incorrect. The file format must be GBSeqXML for CDSParser to read it. The file could be incorrect if your browser is "reading" or interpreting it. Review the Downloading GBSeqXML files section of this manual to download your sequences correctly.
IO Exception occurred while writing file
An IO Exception means that the program encountered an error while trying to write the file. This problem is generally fixed by trying again, and possibly saving in a standard directory with a typical filename.
problem creating file
This error means that the program could not finish writing the file. This problem is generally fixed by trying again, and possibly saving in a standard directory with a typical filename.
name not added because not present in uploaded data set
When group files are loaded, CDSParser verifies that the names in the file were present the previously inputted GBSeq XML file. If a name is not present in the GBSeq XML file, then CDSParser will ignore the name. However, the name will still be present in the group file unless the group file is overwritten.
file not loaded
This error means that CDSParser was not able to load the file. If trying to load the file again does not work, the file is probably corrupt and may need to be resaved.
not a group file
CDSParser will give this error when the user tries to upload a file that does not have the '.grp' extension.
file does not exist
CDSParser will give this error when the user inputs a filename that does not exist on the computer.
error saving groups
This error will occur when CDSParser cannot save a group file. This problem is generally fixed by trying again, and possibly saving in a standard directory with a typical filename.
Sequence errors
Error obtaining sequence
This error will occur when a coding sequence for a gene cannot be calculated because there is no master sequence for the record.
Error calculating sequence
This error will occur when a coding sequence for a gene cannot be calculated because the master sequence consists of links to other GenBank records. CDSParser cannot determine these sequences because it is not set up to access NCBI's database.
Warning: CDS name not added
This warning occurs when a group file is being uploaded. Names that are not present in the currently uploaded data set (GBSeq XML data) will not loaded into the delete set or groups.
ClustalW errors
ClustalW does not execute
There are two reasons ClustalW would not work. First: clustal.def may not have the correct pathname. Verify that ClustalW is installed on your computer, and that the pathname in clustal.def reflects the location of ClustalW's executable. Second: the inputted FASTA file is not in the correct format. This could occur because there are problems with the sequences, or CDSParser has a bug. If you are certain that there are no problems with your sequences and that clustal.def has the correct pathname, send a bug report to CDSParser@byu.edu with the GBSeqXML file, the group file if relevant, and the problematic FASTA file.