Warning/Error Messages
The following scenarios result in a warning or error message.
| • | Manifest file used to generate GTC was not the same as the manifest file used to generate the CN model. |
| • | FASTA files and FASTA index files are out of sync. |
For the following scenarios, the software reports user-actionable messages to the terminal output (as either a warning or an error):
| • | Indel processing for GTC to VCF conversion failed. |
| • | User points to a corrupted input file. |
| • | The input folder does not contain the required input files. |
| • | An input file is corrupt. |
Examples of such notifications can include:
|
Error |
Type |
Cause |
|---|---|---|
|
Reference allele is not queried for locus: {identifier} |
Warning |
True reference allele does not match any alleles in the manifest. The error is common if no MNV defined in Aux loci VCF. |
|
Skipping nonmapped locus: {locus.Name} |
Warning |
Locus has no chromosome position. Array Analysis CLI cannot find the REF and ALT from the genome. |
|
Skipping indel: {locus.Name} |
Warning |
Indel context (deletion/insertion) could not be determined. |
|
Invalid manifest file path {manifestPath} |
Error |
Application could not find manifest file provided or user error. |
|
Failed to load cluster file: {e.Message} |
Error |
Corrupt or unreachable cluster file. |
