Disperse - Frequently Asked Questions

Frequently Asked Questions

General

Troubleshooting

What is the purpose of the SNP data file, and is it required?: The purpose of the SNP data file is to allow PieceMaker to filter out restriction fragments where a restriction site is affected by a known single-nucleotide polymorphism. Also, it can be set to filter out fragments where there are known polymorphisms within the regions that will hybridize to the selector probe. The file is not required, but if it is not present, you need to run the pipeline with the -nosnp option. Or provide an empty snp file in its place.

I get the message "Master variation file does not exist: ...". What's wrong?: If you want to run with the snp option active (which is the default) you need to have a snp data file (master variation file) in the location specified in the configuration file. This can be downloaded from the web site. If you do not want to run with the snp option active, use the -nosnp command line option.
I get the message "Pipeline failed in SNP info generator". What's wrong?: One possible source of this error is that PieceMaker has not been installed properly. Please see the setup instructions.
I get an error message like "Can't locate Log/Log4perl.pm in @INC (@INC contains: ...". What's wrong?: It looks like the Log::Log4perl perl module hasn't been installed properly. Check the setup page for instructions on getting this required module.