Functional Genomics App Errors
This is a list of error messages found within the Job Log for Functional Genomics App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.
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This is a list of error messages found within the Job Log for Functional Genomics App Jobs, what they mean and how to go about fixing them or if a job ticket needs to be submitted.
Last updated
Was this helpful?
UE=User fixable or possible user error
KE=KBase error
UK=Unknown or multiple possibles causes
TE=Temporary system problem
You can always submit a ticket for help, questions, or follow-up to the .
Error running service CLI for method 'ClusterServiceR.cluster_hierarchical' with exit code 1 …...KE: The app is failing and needs maintenance.
Nothing can be done at this time. KBase is working on a solution to this problem.
cannot have both input_one_sequence and input_one_ref parameter UE: The app requires either a single Query Sequence or a Query Object with single sequence.
Change the inputs and try resubmitting the job.
output_one_name parameter required if input_one_sequence parameter is provided UE: If a Query Sequence is used as input, an Output Query Sequence must be named.
Add an output name or change the input. Then try resubmitting the job.
Feature ID AT2G30640 does not exist in the supplied genome UE The selected feature does not exist in the genome.
Recheck the selection and try resubmitting the job.
Error processing genome [xxx/xxx/x] (Not one protein family member found) UE: The species tree is built using the predicted proteins in the genomes.
Run an app that does gene calling/genome annotation on the listed genome(s). Either RAST or Prokka annotation will work.
float division by zero The app will fail with this message if there are only 2 genomes in the pangenome.
Try running the app with 3 or more genomes.
ABORT: You must run the RAST SEED Annotation App or use SKIP option…. UE: The app is expecting RAST annotation for the input genome(s).
The easiest option is to check the 'Skip missing genomes' box in the advanced parameters. For more complete output 1) rune Annotate Microbial Genome(s) with RAST on the listed genomes and 2) use the genome(s) newly created by RAST as the input to the View Function Profile. Because the names are different, the app does not know how to find the newer version of the genome.
ABORT: You must run the 'Domain Annotation' App or use SKIP option …. UE: The app is expecting Domain annotation for the input genome(s).
Either run the Domain Annotation on the listed genome(s) or check the ‘Skip missing genomes’ box in the advanced parameters.
missing or empty krona input file UE: The filters were too restrictive and no output was generated.
Change the input parameters and try resubmitting the job.
(1, '/bin/bash -c "source activate py2 && GTDBTK_DATA_PATH KE: Unknown error.
Nothing can be done at this time. KBase is working on a solution to this problem.
(2, '/bin/bash -c "source activate py2 && GTDBTK_DATA_PATH UE: The ‘Minimum Alignment Percent’ was left blank
Assign a minimum percent in the advanced parameters and try resubmitting the job.
Invalid input:nselect Run All Paired Condition Combinations or provide partial condition pairs. Dont do both UE: The user failed to select ALL vs Partial conditions. It cannot be blank and you cannot select both.
Do one of the following:
Check the box next to 'Run All Paired Condition Combinations.'
Add a 'Run Partial Condition Combinations.'
(2, No such file or directory) UE: The wrong reference database was used.
Change the reference database and try resubmitting the job.
KE: More than two reads libraries were included in the input.
The developers have a task to fix this. The workaround is to only submit a maximum of two libraries at a time. Merging reads libraries can help with this process.
You must enter either an input genome or input reads UE: There are two input options and one of them must be selected.
Add an input and try resubmitting the job.
Cannot write data to fasta KE: The user interface allows users to enter a genome as input but the app will reject it. The error has been reported.
Change to an input that is not a genome and try resubmitting the job.