These are chat archives for dereneaton/ipyrad

31st
May 2017
Bohao Fang
@fangbohao_twitter
May 31 2017 12:05
@isaacovercast Even use the latest version 0.6.24, for Reference and Denovo+Reference methods, step 6 is really slow. (Denovo method is fine/quick). Do you have any idea about it?
Step 6: Clustering at 0.85 similarity across 141 samples
[####################] 100% concat/shuffle input | 0:14:06
[# ] 8% clustering across | 1 day, 16:37:40
I rerun it from step1-7 using the 0.6.24
Isaac Overcast
@isaacovercast
May 31 2017 17:10
@fangbohao_twitter What does your data look like? What do you mean by "fine/quick", how fast does denovo run? How many loci do you get for denovo?
Bohao Fang
@fangbohao_twitter
May 31 2017 19:40
@isaacovercast Thank you for your help!
The data type is single end RAD-seq data, and the consuming time in step 6 for two methods are as below. once before I run step 6 by reference method successfully (in a rational time) by using v. 0.5.**, but there was something wrong with vcf file output. The total_filtered_loci number for denovo-method is 272,942 (v. 0.6.24).
Screen Shot 2017-05-31 at 10.36.27 PM.png
Screen Shot 2017-05-31 at 10.09.35 PM.png
Deren Eaton
@dereneaton
May 31 2017 19:43
thanks @fangbohao_twitter, that's really interesting, we'll try to figure out why it's running so slow in step 6. It should in theory run faster for the reference method.