As part of the latest release of BaseSpace, we have identified a few bugs as follows:
Projects with any character other than alphanumeric, underscore (_), or dash (-), will cause BCL2FASTQ 2.17 to fail. Since the latest BaseSpace release is using the same core algorithms, FASTQ Generation will fail if invalid characters are used. Users will see an error notification, and the log file will have details on the error.
As a temporary workaround: Users can remove the invalid characters OR make sure the column header in the SampleSheet Data section is called SampleProject NOT Sample_Project OR SAMPLE_PROJECT. PrepTab users with NextSeq will need to rename their Projects for the time being. Users will need to manually move Samples to existing Projects from newly created Projects.
For samples that have an underscore (_) in the name, the automatic conversion to a dash (-) in the file name, as occurred previously, is not occurring. As a result, a some apps may fail to launch.
A workaround for the time being is to rename the sample without the underscore, and requeue the FASTQ generation.
IGV is not opening projects and samples, because a BaseSpace API is failing.
We are working towards providing a fix for all of these as soon as possible.