Internal error messages

File and/or directory read/write access permission related error messages:

If you encounter one of the following errors when running j5 from the command line, it is most likely because file and directory permissions in the current working directory prevent j5 from creating new or editing existing files. If you encounter one of the following errors when using j5 with the stand alone simplified web-based interface, it is most likely due to an improperly installed local version of the j5 stand alone simplified web-based interface (contact your IT support staff and/or consult the local installation of j5 documentation page for more information).

Can't change directory back to the parental directory

j5 is unable to change the directory back to the parental directory.

Can't change working directory to directory_name: error_message

j5 is unable to change the working directory to directory_name. The error message may provide additional information.

Can't copy file file_name back to the parental directory

j5 is unable to copy the file file_name to its parental directory.

Can't copy file file_name to the upload directory

j5 is unable to copy the file file_name to the upload directory.

Can't copy j5 input file file_name to directory directory_name: error_message

j5 is unable to copy the j5 input file file_name to directory directory_name. The error message may provide additional information.

Can't create directory directory_name: error_message

j5 is unable to create the directory directory_name. The error message may provide additional information.

Can't extract zipped sequence file file_name to directory directory_name: error_message

j5 is unable to extract the zipped sequence file file_name to directory directory_name. The error message may provide additional information.

Can't open file file_name for writing: error_message

j5 is unable to create the file file_name. The error message may provide additional information.

Can't remove directory directory_name: error_message

j5 is unable to remove the directory directory_name. The error message may provide additional information.

Can't zip j5 working directory directory_name

j5 is unable to zip the j5 working directory directory_name.

Combinatorial assembly output file: Can't open file file_name for writing: error_message

j5 is unable to create the new combinatorial assembly output file file_name. The error message may provide additional information.

Condensed assembly output file: Can't open file file_name for writing: error_message

j5 is unable to create the new condensed assembly output file file_name. The error message may provide additional information.

Master direct syntheses list file: Can't open file file_name for appending: error_message

j5 is unable to append new direct syntheses pieces to the master direct syntheses list file file_name. The error message may provide additional information.

Master oligos list file: Can't open file file_name for appending: error_message

j5 is unable to append new oligos to the master oligos list file file_name. The error message may provide additional information.

Master plasmids list file: Can't open file file_name for appending: error_message

j5 is unable to append the newly designed plasmid(s) to the master plasmids list file file_name. The error message may provide additional information.

New j5 assembly file: Can't write to file file_name: error_message

j5 is unable to write the new assembly file file_name. The error message may provide additional information.

Local installation related error messages:

If you encounter one of the following errors, it is most likely due to an improperly installed local version of the j5 package. Contact your IT support staff and/or consult the local installation of j5 documentation page for more information.

Cannot use Text::CSV package: error message

j5 is unable to successfully call the Text::CSV perl module to parse a comma separated value (CSV) file. Check your local installation of Text::CSV, and make sure it meets the requirements of j5. The error message may provide additional information.

Primer3 executable can not be found at PRIMER3PATH

j5 is unable to successfully call the Primer3 executable at the specified path PRIMER3PATH. Check your local installation of Primer3, and make sure it meets the requirements of j5. The path to Primer3 is specified in the perl module file j5/Configuration.pm.

Command-line interface error messages:

If you encounter one of the following errors, it is most likely due to specifying too many or too few j5 input files on the command line.

Usage: j5_program j5ParametersFileName SequencesListFileName PartsListFileName TargetPartOrderListFileName MasterPlasmidsListFileName MasterOligosListFileName MasterDirectSynthesesListFileName

The j5 perl script j5_program expects seven j5 input files to be specified on the command line (as suggested in the error message). Make sure that you have specified the correct number of input files. Four j5 perl scripts (j5_SLIC_Gibson_CPEC.pl, j5_golden_gate.pl, j5_combinatorial_SLIC_Gibson_CPEC.pl, and j5_combinatorial_golden_gate.pl) have this same command line usage.

Usage: j5_program j5ParametersFileName SequencesListFileName ZippedSequencesFileName PartsListFileName TargetPartOrderListFileName MasterPlasmidsListFileName MasterOligosListFileName MasterDirectSynthesesListFileName

The j5 perl script j5_program expects eight j5 input files to be specified on the command line (as suggested in the error message). Make sure that you have specified the correct number of input files. Four j5 perl scripts (j5_SLIC_Gibson_CPEC_zip.pl, j5_golden_gate_zip.pl, j5_combinatorial_SLIC_Gibson_CPEC_zip.pl, and j5_combinatorial_golden_gate_zip.pl) have this same command line usage.

Usage: j5_program AssemblyFilesToCondenseFileName

The j5 perl script j5_program expects one j5 input file to be specified on the command line (as suggested in the error message). Make sure that you have specified the correct number of input files. The j5 perl scripts j5_condense_assembly_files.pl has this command line usage.

Usage: j5_program AssemblyFilesToCondenseFileName ZippedAssemblyFilesFileName

The j5 perl script j5_program expects two j5 input files to be specified on the command line (as suggested in the error message). Make sure that you have specified the correct number of input files. The j5 perl scripts j5_condense_assembly_files_zip.pl has this command line usage.

Other internal error messages:

If you encounter one of the following errors, it is most likely due to an internal bug within j5. Please contact the j5 development team with details so that we can fix the problem.

Combinatorial design: Can't open file template assembly file file_name: error_message

j5 is unable to open the combinatorial template assembly file file_name. It is likely that the template assembly design did not complete correctly. The error message may provide additional information.

Combinatorial design: Can't open condensed assembly file file_name: error_message

j5 is unable to open the condensed assembly file file_name that results from condensing each individual combinatorial assembly. It is likely that condensing the individual assembly files did not complete correctly. The error message may provide additional information.

Convert_Mac_Carriage_Returns: Can't open file file_name: error_message

j5 is unable to open the file file_name to replace mac-style carriage returns with standard new line returns. The error message may provide additional information.

Golden-gate design: 3' overhang of assembly piece upstream_piece (sequence upstream_sequence) does not match the 5' overhang of assembly piece downstream_piece (sequence downstream_sequence)

j5 has erringly designed a Golden Gate assembly that results in two neighboring assembly pieces, namely upstream_piece and downstream_piece, that do not having matching Golden Gate overhangs. The overhang sequences at the ends of the two pieces, upstream_sequence and downstream_sequence, are displayed.

SLIC/Gibson/CPEC design: 3' end of assembly piece this_piece does not match 5' end of assembly piece the_next_piece

this_piece_3'_sequence the_next_piece_5'_sequence j5 has erringly designed a SLIC/Gibson/CPEC/SLiCE assembly that results in two neighboring assembly pieces, namely this_piece and the_next_piece, that do not having matching sequence homology overlap regions. The ends of the two sequences, this_piece_3'_sequence and the_next_piece_5'_sequence, are displayed.

j5 XML-RPC web service specific error messages:

j5_XML_RPC: Invalid username or password

A valid username and password is required for creating a new j5 session ID. Accounts are available at the j5 website's request an account page.

j5_XML_RPC: method method_name not recognized...

The requested method, method_name, was not recognized. The set of implemented method names is provided on the j5 XML-RPC web services page.

j5_XML_RPC: session id j5_session_id is invalid or has expired. Please use the XML-RPC method CreateNewSessionId to obtain a valid j5 session id...

The session id j5_session_id passed as a parameter to the XML-RPC web service method was either invalid, or has expired. A valid session id must be used when calling the j5 XML-RPC web services.

j5_XML_RPC: DesignAssembly: assembly method assembly_method is not recognized

The assembly method assembly_method was not recognized when calling the XML-RPC method DesignAssembly. The set of implemented assembly methods is provided on the j5 XML-RPC web services page.

j5_XML_RPC: DesignDownstreamAutomation: automation task automation_task is not recognized

The automation task automation_task was not recognized when calling the XML-RPC method DesignDownstreamAutomation. The set of implemented assembly methods is provided on the j5 XML-RPC web services page.