These are chat archives for dereneaton/ipyrad

17th
Jul 2018
Isaac Overcast
@isaacovercast
Jul 17 2018 00:02
@spirospapakostas Well, it could depend on a lot of things. If the assembly is not very good, then maybe you have lots of very short contigs, and you might get lots of reads with multiple hits to the reference sequence. This maybe isn't clear from the docs, but reads with more than one unique hit are dropped from the reference pipeline, and not retained for denovo. All reads that do not match to the reference are denovo clustered, but reads that match multiple times are removed, on the assumption that these are paralogs.
Still 90% reduction of loci in the final assembly is pretty extreme. I'd have to see the stats files for the denovo and the denovo+reference assemblies to give you a better idea.
@yulietacevedo_twitter Are you using --MPI?
Also, where are you getting the RuntimeWarning from? Does it print to the screen? It doesn't show up in the error copied and pasted from the ipyrad command, so it's hard to know whether how it relates to the TimeoutError.
@tommydevitt Which part of the structure cookbook are you running that isn't doing what you think it should be? Did you copy the jupyter notebook from the repository?
tommydevitt
@tommydevitt
Jul 17 2018 02:12
@isaacovercast The quick guide section. I downloaded the notebook from http://nbviewer.jupyter.org/github/dereneaton/ipyrad/blob/master/tests/cookbook-structure-pedicularis.ipynb