These are chat archives for dereneaton/ipyrad

Mar 2017
Bohao Fang
Mar 20 2017 11:23
As a outcome file, vcf file doesn't have positon information but I can only see "."; Where can I get postion infomation? Thank you!! BTW, im running the latest version 0.6.10.
Amanda Haponski
Mar 20 2017 14:33
I am interested in doing the ABBA-BABA tests on my dataset. Has this been implemented in ipyrad yet? Thanks in advance.
Bohao Fang
Mar 20 2017 14:57
I mean in vcf file the #CHOM name is still "locus_XXX" but not chromosome name. Is there anything wrong with this lastest vcf file?
Emily Warschefsky
Mar 20 2017 17:30
@dereneaton @isaacovercast - I finished an analysis for steps 1-7 at clust 0.95, and then branched to rerun from step 3 at clust 0.90. Running in parallel across 32 cores, the analysis has been stuck at 56% clustering for almost 5 days. Also, none of the htemp or utemp files in the "clust" folder have been written to in 5 days - is there another set of files somewhere that I should be looking at to see if the run has progressed at all?
Isaac Overcast
Mar 20 2017 18:52
@fangbohao_twitter Did you do a 'reference' or 'denovo+reference' assembly?
Isaac Overcast
Mar 20 2017 19:49
@ewarschefsky_twitter How long did step 3 take for the 0.95 threshold? I assume it was faster than 5 days or it wouldn't raise an eyebrow.... There is a directory called watever_clust_0.9right? If you do an ls -ltr in this directory it should show you all the files that have been most recently modified. There should be .clust.gz or .clustS.gz files getting updated in this directory.
Let me know what you see in there.
Mar 20 2017 21:22
@dereneaton I was wondering if there was anywhere in the output files where it says the number of merged reads. In the old ipyrad version I did this based on the .merged file from s3, but I dont see this output file anymore. Thanks for the help!