These are chat archives for dereneaton/ipyrad

14th
Feb 2017
Amanda Haponski
@ahaponski_twitter
Feb 14 2017 19:08
Hi @dereneaton. I have just completed my first denovo assembly in ipyrad and I have a few individuals that did not sequence well and need to be dropped. Is there anyway to remove them from my current analysis or do I have to do a new assembly? I did try to create a population assignment file and did not include those individuals in my populations, but they still appeared in my final outputs. Thanks in advance!!!!
Deren Eaton
@dereneaton
Feb 14 2017 19:15
@ahaponski_twitter Yes they can easily be dropped by subsampling during 'branching'. Example:
## create a new branch dropping samples A and B (list names to drop
## after the "-" character after the new assembly name)
ipyrad -p params-oldassembly.txt -b newassembly - A B 

## OR, list only the names you want to keep by listing them after the
##  branch name without a "-" character
ipyrad -p params-oldassembly.txt -b newassembly C D E F

## proceed with new assembly in step 7 (use force flag b/c 
## the previous assembly had finished step 7). New files will
## have the new assembly name as a prefix. 
ipyrad -p params-newassembly.txt -s 7 -f
Alexander McKelvy
@SnakeEvolution_twitter
Feb 14 2017 20:57

Hi guys. Fresh install of iPyrad using a data set/param file that has worked plenty of times before, Step one completes, followed by this:

Step 2: Filtering reads
[####################] 100% processing reads | 0:12:08
found an error in step2; see ipyrad_log.txt

Any ideas what to try first? Thanks!