These are chat archives for dereneaton/ipyrad

15th
Feb 2018
kyule
@kyule
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
@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.
dionyes
@dionyes
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
@dereneaton
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?
dionyes
@dionyes
Feb 15 2018 22:29
Hi @dereneaton , so I've been using "wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh" 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