These are chat archives for dereneaton/ipyrad

24th
Jun 2016
danielyao12
@danielyao12
Jun 24 2016 02:08
This message was deleted

@isaacovercast I installed the latest version of conda (4.1.3) and ipyrad (0.3.10), while I met problems when I run step1 according to the Introductory tutorial. The error messages are:--------------------------------------------------
ipyrad [v.0.3.10]

Interactive assembly and analysis of RADseq data

New Assembly: iptest
Traceback (most recent call last):
File "/lustre/home/yaoxin/miniconda2/bin/ipyrad", line 9, in <module>
load_entry_point('ipyrad==0.3.10', 'console_scripts', 'ipyrad')()
File "/lustre/home/yaoxin/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 430, in main
data = getassembly(args, parsedict)
File "/lustre/home/yaoxin/miniconda2/lib/python2.7/site-packages/ipyrad/main.py", line 237, in getassembly
data.set_params(param, parsedict[param])
File "/lustre/home/yaoxin/miniconda2/lib/python2.7/site-packages/ipyrad/core/assembly.py", line 648, in set_params
param = self.paramsdict.keys()[int(param)]
IndexError: list index out of range
Do you know how can I fix this problem? Thanks in advance! And I have to say that the ipyrad is much easier to install than pyrad.

Isaac Overcast
@isaacovercast
Jun 24 2016 03:28
@danielyao12 Are you running it from the command line? If so, it looks like there's a problem with the params file. Will you email me a copy of your params file so I can check it out? iovercast@gc.cuny.edu
danielyao12
@danielyao12
Jun 24 2016 03:41
@isaacovercast Thanks for your help! I have send the params file to you.
Isaac Overcast
@isaacovercast
Jun 24 2016 03:42
Cool. give me a minute to check it out. did you see deren's talk at evolution?
danielyao12
@danielyao12
Jun 24 2016 03:45
@isaacovercast I don't see deren's talk. Could you please tell me where I can find? I saw his website about pyrad and read all tutorials on his website.
Isaac Overcast
@isaacovercast
Jun 24 2016 03:46
oh, yeah, i just mean his talk at evolution a couple days ago, i don't think its online yet.
danielyao12
@danielyao12
Jun 24 2016 03:52
@isaacovercast Too bad, I cann't get there.
Isaac Overcast
@isaacovercast
Jun 24 2016 03:54
I see the problem, very easy to fix.
Isaac Overcast
@isaacovercast
Jun 24 2016 03:59
Sent you an email with the fix.
Cycadales
@Cycadales
Jun 24 2016 04:02
@isaacovercast did you mange to replicate the issue in step 1?
Isaac Overcast
@isaacovercast
Jun 24 2016 04:03
Yeah, for sure. It appears to be hanging. The background process is consuming 100% cpu but im not sure what its doing at this point. I'll know more soon.
Cycadales
@Cycadales
Jun 24 2016 04:05
@isaacovercast Ahh excellent! well not for the bug...
danielyao12
@danielyao12
Jun 24 2016 05:12
@isaacovercast Thanks very much! It runs well following your suggestions, but I meet new problems when I run step 6. I send the error messages to you. Could you please have a look if you have time?
Isaac Overcast
@isaacovercast
Jun 24 2016 18:34
NB: Step 6 is broken in 0.3.10. I pushed a new version that fixes step 6 (0.3.11) please upgrade.