Just switched to ipyrad from pyrad - am working with ipyrad v. 5.3 and have a couple of questions.
1) I ran the introductory single-end rad-seq tutorial and the tutorial with the Eaton + Ree (2013) dataset (ran both tutorials twice with the same parameter settings). All steps ran fine, but the numbers in the final stats output (e.g. number of filtered reads, loci recovered for each sample, distribution of snps across loci etc. ) are similar but not identical to the numbers actually shown in the documentation for the tutorials. Ditto for the content of the output files (e.g. length of concatenation in the phy file differs between my runs and the the documentation). This is to be expected isn't (i.e. results should be approximately the same not precisely the same)?
2) The output files do not include the nexus, .geno and .u.geno files, and the vcf file has the fomat vcf (not vcf.gz). Is there a simple fix for this? E.g. can I list all the different file formats individually in the params file?