j5 input error messages

j5 input file specific error messages:

Combinatorial target part order list file: Can't open file file_name: error_message

j5 is unable to open the combinatorial target part order list file file_name. Check to make sure that file_name matches the name of a combinatorial target part order list file in the current working directory (if calling j5 from the command line), or that you specified a combinatorial target part order list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Combinatorial target part order list file: part_name appears to be a part name, but it appears in the list before any combinatorial bin. Either correct this, or if you intended to design a single construct, please use j5's "Mock Assembly", "SLIC/Gibson/CPEC Assembly" or "Golden Gate Assembly" design option instead of "Combinatorial Mock Assembly", "Combinatorial SLIC/Gibson/CPEC Assembly" or "Combinatorial Golden Gate Assembly" design.

The name of a part, part_name, in the combinatorial target part order list file appears before the definition of a combinatorial bin. This message is generated during combinatorial construct assembly design. Perhaps you intended to design a single construct Mock Assembly, SLIC/Gibson/CPEC/SLiCE or Golden Gate assembly instead?

Combinatorial target part order list file: target bin bin_number ("bin_name"), contains no parts. Exiting...

The target bin bin_number (whose name is bin_name) contains no target parts.

Downstream automation parameters file: Can't open file file_name: error_message

j5 is unable to open the downstream automation parameters file file_name. Check to make sure that file_name matches the name of a downstream automation parameters file in the current working directory (if calling j5 from the command line), or that you specified a j5 parameters file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

j5 assembly file: Can't open file file_name: error_message

j5 is unable to open the j5 assembly file file_name. Check to make sure that file_name matches the name of a j5 assembly file in the current working directory (if calling j5 from the command line), or that you specified a j5 assembly file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

j5 parameters file: Can't open file file_name: error_message

j5 is unable to open the j5 parameters file file_name. Check to make sure that file_name matches the name of a j5 parameters file in the current working directory (if calling j5 from the command line), or that you specified a j5 parameters file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

j5 parameters file: the specified type IIs endonuclease recognition sequence (GOLDENGATERECOGNITIONSEQ, "golden_gate_recognition_sequence") is not found within the specified sequence to be added to the termini of each Golden Gate assembly piece (GOLDENGATETERMINIEXTRASEQ "golden_gate_termini_extra_sequence").

The specified type IIs endonuclease recognition sequence golden_gate_recognition_sequence (e.g. GGTCTC for BsaI) is not contained within the golden gate termini extra sequence golden_gate_termini_extra_sequence (e.g. CACACCAGGTCTCA). Perhaps you changed the golden gate recognition sequence for a different type IIs endonuclease (e.g. for BsmBI, to CGTCTC), but forgot to make the corresponding changes to the golden gate termini extra sequence (e.g. for BsmBI, to CACACCACGTCTCA)?

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

j5 is unable to open the master direct syntheses list file file_name. Check to make sure that file_name matches the name of a master direct syntheses list file in the current working directory (if calling j5 from the command line), or that you specified a master direct syntheses list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

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

j5 is unable to open the master oligos list file file_name. Check to make sure that file_name matches the name of a master oligos list file in the current working directory (if calling j5 from the command line), or that you specified a master oligos list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

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

j5 is unable to open the master plasmids list file file_name. Check to make sure that file_name matches the name of a master plasmids list file in the current working directory (if calling j5 from the command line), or that you specified a master plasmids list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Multi-well plate file: Can't open file file_name: error_message

j5 is unable to open the multi-well plate file file_name. Check to make sure that file_name matches the name of a multi-well plate file in the zipped source plates file. The error message may provide additional information.

One or more j5 input files not specified for upload or last-updated selected for re-use

Check to make sure that you either specified all input files for upload (or selected to re-use the last updated versions) when using the stand alone simplified web-page interface for j5.

Parts list file: Can't open file file_name: error_message

j5 is unable to open the parts list file file_name. Check to make sure that file_name matches the name of a parts list file in the current working directory (if calling j5 from the command line), or that you specified a parts list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Parts list file: Definition of part part_name: Sequence display ID sequence_display_ID does not match a sequence contained within the sequence files listed in the sequences list file.

In the parts list file, in the row defining the part part_name, the sequence display ID does not match that of any of the sequences contained in the sequence files listed in the sequences list file. Note that the sequence display ID (the text that immediately follows the ">" character in FASTA files or the first field on the "LOCUS" line in Genbank files) is not necessarily the same as the name of the sequence file that contains the sequence. To check the sequence display ID for a given sequence file, open he sequence file with a text editor (such as notepad or TextEdit).

Parts list file: Two parts have the same name: part_name

In the parts list file, two or more parts have the same name (part_name). Make sure that each defined part has a unique name.

Sequences list file: Can't open file file_name: error_message

j5 is unable to open the sequences list file file_name. Check to make sure that file_name matches the name of a sequences list file in the current working directory (if calling j5 from the command line), or that you specified a sequences list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Sequences list file: Sequence file type must be "FASTA" or "Genbank". file_format is not a valid file format

In the sequences list file, the sequence file format must be either "FASTA" or "Genbank".

Sequences list file: Two sequences have the same sequence display ID: sequence_display_ID

The sequence display IDs (the text that immediately follows the ">" character in FASTA files or the first field on the "LOCUS" line in Genbank files) of two or more sequences is identical. Note that two sequence files with distinct file names can contain sequences with identical display IDs. Open the each of the sequence files listed in the sequences list file with a text editor (such as notepad or TextEdit), and check to see which the files contain sequences with identical display IDs (e.g. sequence_display_ID), and make sure that each sequence has a unique display ID.

Source plates list file: Can't open file file_name: error_message

j5 is unable to open the source plates list file file_name. Check to make sure that file_name matches the name of a source plates list file in the current working directory (if calling j5 from the command line), or that you specified a source plates list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Target part order list file: Can't open file file_name: error_message

j5 is unable to open the target part order list file file_name. Check to make sure that file_name matches the name of a target part order list file in the current working directory (if calling j5 from the command line), or that you specified a target part order list file to upload (if using the stand alone simplified web-page interface for j5). The error message may provide additional information.

Target part order list file: part_name appears to be a combinatorial bin name. Please use j5's "Combinatorial SLIC/Gibson/CPEC Assembly" or "Combinatorial Golden Gate Assembly" design option instead of single construct "SLIC/Gibson/CPEC" or "Golden Gate Assembly" design.

The name of a part, part_name, in the target part order list file begins with the character '>', which is used to designate a combinatorial bin name during the combinatorial SLIC/Gibson/CPEC/SLiCE or Golden Gate design process (see the target part order list input file documentation for more information). This message is generated during single construct SLIC/Gibson/CPEC/SLiCE or Golden Gate assembly design. Perhaps you intended to design a Combinatorial SLIC/Gibson/CPEC/SLiCE or Golden Gate assembly instead?

Target part order list file: part_name not found in the parts list

The part part_name in the target part order list file is not defined within the parts list file. Check to make sure that the part name in the target part order list file exactly matches that in the parts list file.

Target part order list file: DIGEST forced assembly strategy may only be set for the first target part

Only the first part in the target part order list file may be forced to use the "DIGEST" assembly strategy.

Target part order list file: forced_assembly_strategy is not a recognized forced assembly strategy

The only allowable options for forced assembly strategies are "DIGEST", "PCR", "Direct Synthesis", "Embed_in_primer_forward", "Embed_in_primer_reverse", "unspecified", and empty.

Zipped sequences file: sequence file sequence_file_name not found within the zip_file_name zip file

j5 is unable find the sequence file sequence_file_name that is listed in the sequences list file within the zipped sequences file zip_file_name. Check to make sure that sequence_file_name is contained within the zip file.