These are chat archives for dereneaton/ipyrad

Feb 2018
Feb 15 2018 19:02
@isaacovercast I'm still unable to make it through step 3 with my ddRAD, 2x150 data (96 samples, ~220 GB) with which I am trying to identify loci for a RAD capture study. Running on an HPC (28 cores), the clustering appears to go fairly quickly but slows down dramatically once it reaches >95% to the point that it almost seems to take exponentially longer for each additional percent. It just spent 7 days running at 97% (on just a subset of my individuals with the best data) before I ran out of compute time. The problem may be low quality scores towards the ends of the reads leading to variable length reads (basing this on fastqc results and losing a lot of reads for falling below the minlength). When I increase the quality control parameters to only allow better reads to get through, all steps finish quickly but I get very low numbers of loci per individual. Do you have any suggestions for how to proceed to be able to move past step 3?
Eaton Lab
Feb 15 2018 19:06
@kyule, you're right about low quality ends increasing the number of unique reads and therefore increase the total clustering time. However, if your analyses runs quickly up to 95% and then slows down, it is probably that you have one or two samples with 100X more data than the others, and it's just taking a long time to finish those samples. You could subsample data from those samples, so they are more like the other ones, or just run them on a separate branch and let them run however long it takes and then merge them back in with your other samples before step 6.
Feb 15 2018 20:32
@eaton-lab Hello! I've been trying to install ipyrad onto a linux machine, and I have run into some issues where it won't access the url. I've also found that I can't access the ipyrad website from any browser on the linux machine. Do you guys have any recommendations? Thanks so much!
Deren Eaton
Feb 15 2018 20:42
Hi @dionyes , we do almost all of our testing and development on linux, and I'm using it now and all is working, so I think the problem may be specific to your machine or the commands you are using. What url are you trying to access?
Feb 15 2018 22:29
Hi @dereneaton , so I've been using "wget" but it will just say connection failure. I've also noticed that I can't open any sections of the ipyrad website when I see it in google. The cursor just spins and says time out. I have been able to open it/download everything on a mac on the same network. I also tried downloading anaconda from the online site and then i tried to update conda and install ipyrad but it kept saying connection failure