====== Errors and Solutions ======

====== Mark as pass in Geneious-Biocode: ======

The error may occur when passing the consensus sequences:

{{:geneious:geneious_pass_lims_data_not_found.png|}}

This may be due to the fact that either the link to the LIMS/FIMS data has been lost in the assembly or in the raw data document, or the annotation with LIMS/FIMS data has not yet been executed. The following can help:

  - Check if the of the assembly document is the AccessionNumber + '_' + Assembly. If not: Rename (or batch rename for multiple documents)
  - Annotate with LIMS/FIMS data again for the assembly document
  - Mark as pass should now work
  - If not: Repeat annotation with FIMS/LIMS data for the document in the raw data folder.

The whole process can also be carried out for several documents at the same time. Simply select all those that contain errors and perform the operations.

====== Batch Rename ======

Several documents can be renamed at once. In the example, the space in the document name is replaced by an underscore: ''CaBOL-1027032 Assembly'' -> ''CaBOL-1027032_Assembly'':

  - Select the documents to be renamed
  - Select Edit -> Batch Rename from the navigation menu
  - From ''Aspect to Rename:'' choose ''Fields of Document''
  - ''Field to rename:'': Name
  - Click ''Advanced''
  - Check ''Replace parts matching:'' and in the input field enter ''\s'' (= space)
  - Check ''Regex''
  - In the field ''With:'' enter ''_'' (underscore)
  - Click ''OK''

{{:geneious:batch_rename_assembly.png|}}