These are chat archives for dereneaton/ipyrad

Aug 2017
Aug 25 2017 07:48

@toczydlowski Yes I did but that's where it looks weird to me in the first section "assembly": { "dir": {"clusts" is pointing towards only one of my clusts folder. I would have expected that it would either merge them into one folder or that this line would point to the different folders.
But then in the second section "samples"is pointing to the right clusts folder for each individual.

What should I modify? Is it possible to indicate multiple locations for clusts in the first section or should I just move the different files to one single location that I would describe there. Then what about the samples section should I modify that too?

Glib Mazepa
Aug 25 2017 12:04
Hi @dereneaton and @isaacovercast, I am running v 0.6.9 with denovo+reference, around a day ago it started to report errors in the log file alike: 2017-08-25 12:44:57,229 pid=50393 [] ERROR Failed get reads at a locus, continuing; list index out of range . It never happened before. Does it mean that something had happenned to the reference index and I need to build a new index or there is something version specific message??? The rest of the steps were finished without issues, but when I ran ADMIXTURE on the .geno output - it gives somewhat weird results...
Deren Eaton
Aug 25 2017 15:11
Hey @zacforsman, the --preview mode has actually been deprecated for a little while now, we just haven't removed it yet -- so maybe you actually ran the whole data set. We have been running speed tests against ddocent for a while now while we work on the manuscript, and ipyrad consistently runs faster in our tests, but like I said, we haven't been testing with PE Miseq reads. But I think you may find that it runs much faster now with the paired reads set up like in the notebook I sent, which in that example data set runs in about 30 seconds. I'll be interested to hear how it goes.
The forming of long contigs in the ez-rad data does make things complicated, though, and it's hard to predict the effect that will have.
Deren Eaton
Aug 25 2017 15:21
@joqb I found the error, fixing it now.
Aug 25 2017 16:09
@dereneaton Ok cool. In the mean time I manipulated the json file to proceed now it's happily running through step 6.
BTW It happened again that my json file got blanked. Hopefully I had a backup as I was planning to play around with it. #255 +1