Annotation App Errors

This is a list of error messages found within the Job Log for Annotation App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.

Types of Errors

• UE=User fixable or possible user error

• KE=KBase error

• UK=Unknown or multiple possibles causes

• TE=Temporary system problem

Use your Browser's search tool to paste in your error message to locate your error message, information about the error and next steps.

You can always submit a ticket for help, questions, or follow-up to the KBase Help Board.

Common Errors across Annotation Apps

RAST: Annotate Microbial Genome / Annotate Multiple Microbial Genomes / Annotate Microbial Assembly / Annotate Multiple Microbial Assemblies

Prokka: Annotate Assembly and Re-annotate Genomes with Prokka

(2, No such file or directory)

UE: One or more contigs had header lines longer than 37 characters.

Edit the fasta file, upload again, and try resubmitting the job.

Error invoking method call_features_rRNA_SEED

UE: One or more of the FASTA header lines are extremely long.

Shorten them, re-upload, and try resubmitting the job. .

Object #1, 0ae7adb1-6351-4d26-a526-cc09c15e46ee.report has invalid reference: ….

UE: There are no input datasets listed.

Supply the dataset(s) and try resubmitting the job.

too many contigs

UE: RAST has a limit of 10,000 contigs. Prokka has a limit of 30,000 contigs.

Divide the file or bin the contigs before running RAST again by resubmitting the job.

Error on ObjectSpecification #1: Unable to parse version portion of object reference nnnn/2/1, nnnn to an integer

UE: The wrong delimiter was used in the free text of the Assembly list or Genome list.

Change the delimiter to a semicolon (;) and try resubmitting the job.

Error on ObjectSpecification #1: Illegal number of separators /

UE: The wrong delimiter was used in the free text of the Assembly list or Genome list.

Change the delimiter to a semicolon (;) and try resubmitting the job.

name assembly_info is not defined

UE: You are running the beta version of the app.

Change to the released version.

Annotate Plant Transcripts with Metabolic Functions

The genome does not contain any CDSs or features!

UE: The input genome does not have the needed features.

Double check the file and try resubmitting the job.

Assess Genome Quality with CheckM

Object NNN cannot be accessed: User user_name may not read workspace XXXXX

UE: The app requires data which is owned by another user and you do not have access. In another scenario, either you or the user have deleted the original assembly.

Ask the user for access to the needed file.