These are chat archives for dereneaton/ipyrad

7th
May 2018
Anna Page
@annampage_twitter
May 07 2018 12:02
@isaacovercast Have you had any more thoughts about the error I described above? I'm using the most recent version (0.7.4) and still getting the same error
Nathan Jones
@insectnate
May 07 2018 15:42

I get the interactive assembly to start but then receive this error. ' -------------------------------------------------------------
ipyrad [v.0.7.24]

Interactive assembly and analysis of RAD-seq data

Traceback (most recent call last):
File "/home/anaconda3/bin/ipyrad", line 11, in <module>
load_entry_point('ipyrad==0.7.24', 'console_scripts', 'ipyrad')()
File "/home/anaconda3/lib/python2.7/site-packages/ipyrad/main.py", line 576, in main
data = getassembly(args, parsedict)
File "/home/anaconda3/lib/python2.7/site-packages/ipyrad/main.py", line 267, in getassembly
data = ip.load_json(assembly_file, cli=True)
File "/home/anaconda3/lib/python2.7/site-packages/ipyrad/load/load.py", line 183, in load_json
fullj = json.loads(infile.read(), object_hook=_tup_and_byte)
File "/home/anaconda3/lib/python2.7/json/init.py", line 352, in loads
return cls(encoding=encoding, **kw).decode(s)
File "/home/anaconda3/lib/python2.7/json/decoder.py", line 364, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/anaconda3/lib/python2.7/json/decoder.py", line 382, in raw_decode
raise ValueError("No JSON object could be decoded")
ValueError: No JSON object could be decoded'

Nathan Jones
@insectnate
May 07 2018 16:35
I was trying to run the first two steps of the piepline i.e. ipyrad -p ipyrad_params -s 12
Rebecca Tarvin
@frogsicles_twitter
May 07 2018 19:02
Hi @dereneaton and @isaacovercast - I was just wondering if there is any plan to speed up step 6 in the near future? iPyrad is such a wonderful resource, but I am coming up against a wall (pun intended) trying to analyze my data within allowable supercomputing wall-time. I've tried all sorts of work-arounds but cannot get step 6 to finish within 48hr. Thanks, -Becca