These are chat archives for dereneaton/ipyrad

3rd
Jun 2017
Isaac Overcast
@isaacovercast
Jun 03 2017 01:33
@cwessinger Sometimes these name error issues are the result of a goofy install. I would try removing and then reinstalling ipyrad. conda remove ipyrad; conda install -c ipyrad ipyrad
@mav1234 @cwessinger is correct, even if it's demux'd you still have to run step 1 so ipyrad can read in the fastq files and also create the assembly. Let me know if you have any questions after you run through the tutorial.
cwessinger
@cwessinger
Jun 03 2017 13:09
@isaacovercast I'm still getting the same error. Strange. This is version 0.6.26. I'll try removing again and reinstalling...
mav1234
@mav1234
Jun 03 2017 17:10
@isaacovercast Hi Isaac, I am still getting the error in the first step of the tutorial; I installed miniconda in my root directory as suggested by the installation instructions and typing ipyrad in my console does display the help menu. I'm running on hpc, and am source activating root. JSON error occurs whether I am in an interactive job or batch submission. It may be something dumb on my part - so my apologies in advance if so!
cwessinger
@cwessinger
Jun 03 2017 17:30

My fullcomp error is persistent. Here is the tail of my logfile. Any ideas? Thanks for the help!!!


ipyrad [v.0.6.26]

Interactive assembly and analysis of RAD-seq data

Begin run: 2017-06-03 08:48
Using args {'preview': False, 'force': True, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 8, 'params': 'params-phy.txt', 'branch': None, 'steps': '67', 'debug': False, 'new': None, 'MPI': False}
Platform info: ('Linux', 'n482', '2.6.32-504.23.4.el6.x86_64', '#1 SMP Fri May 29 10:16:43 EDT 2015', 'x86_64')2017-06-03 12:09:39,172 pid=2712 [cluster_across.py] ERROR NameError(global name 'fullcomp' is not defined)
2017-06-03 12:09:39,311 pid=2712 [assembly.py] ERROR IPyradWarningExit: NameError(global name 'fullcomp' is not defined)

Isaac Overcast
@isaacovercast
Jun 03 2017 18:38
@cwessinger I can't reproduce this error, even in a fresh install in a clean environment. There must be something weird about your python environment. What version of python are you using? Try this python -V
@mav1234 Can you show me the exact step 1 command you're running and the output? You might try running step 1 and including the -f flag, which will force overwrite any bad files hanging around.
Isaac Overcast
@isaacovercast
Jun 03 2017 18:52
@cwessinger I just pushed a new version that will probably fix this problem (0.6.27). Try pulling it down and running step 6 again conda install -c ipyrad ipyrad
mav1234
@mav1234
Jun 03 2017 19:02

@isaacovercast The command is : ipyrad -p params.txt -s 1 ... There are no directories or anything, and I don't think any bad flags. First time trying to run ipyrad. Error is this: -------------------------------------------------------------
ipyrad [v.0.6.26]

Interactive assembly and analysis of RAD-seq data

Traceback (most recent call last):
File "/home/js3633/miniconda2/bin/ipyrad", line 11, in <module>
load_entry_point('ipyrad==0.6.26', 'console_scripts', 'ipyrad')()
File "/home/js3633/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 528, in main
data = getassembly(args, parsedict)
File "/home/js3633/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 256, in getassembly
data = ip.load_json(assembly_file)
File "/home/js3633/miniconda2/lib/python2.7/site-packages/ipyrad/load/load.py", line 168, in load_json
fullj = json.loads(infile.read(), object_hook=_tup_and_byte)
File "/home/js3633/miniconda2/lib/python2.7/json/init.py", line 352, in loads
return cls(encoding=encoding, **kw).decode(s)
File "/home/js3633/miniconda2/lib/python2.7/json/decoder.py", line 364, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/js3633/miniconda2/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

ack that was a long paste... sorry.
cwessinger
@cwessinger
Jun 03 2017 20:25
@isaacovercast How mysterious! python version: Python 2.7.13. Great! I'll give it a try right now! I really appreciate the support!