These are chat archives for dereneaton/ipyrad

2nd
Jun 2016
Isaac Overcast
@isaacovercast
Jun 02 2016 16:23
Hi Robin. I'll take a look at it.
Isaac Overcast
@isaacovercast
Jun 02 2016 17:05
I have a hunch. Can you tell me the version of numpy the cluster is using? If you do qsub -I it'll give you an interactive shell on a compute node. Then you can python and import numpy and numpy.version.version
Isaac Overcast
@isaacovercast
Jun 02 2016 17:15
Also, did you install the conda package or clone the git repo?
Isaac Overcast
@isaacovercast
Jun 02 2016 17:32
Also, in your project directory should be a file that ends with .json, can you email me a copy of that file? isaac.overcast@gmail.com
Isaac Overcast
@isaacovercast
Jun 02 2016 19:14
Ugn. fml. Nasty nasty bug assembly prevented max_shared_Hs_locus param from being read in right. OUch. Cost me an hour of my life.
Robin Sleith
@R0cknRobin_twitter
Jun 02 2016 21:00
Yikes. Should I give it a try now?
Isaac Overcast
@isaacovercast
Jun 02 2016 21:02
Lol, sorry i was more publicly venting about a different problem. max_shared_Hs_locus is a filter for step 7. I'm still looking into your prob with step 5, hang on one sec...
Looks like you're doing a preview run.
Isaac Overcast
@isaacovercast
Jun 02 2016 21:23
I see the problem.
Step 4 is failing and not reporting it properly. In your json file: "error_est":NaN, should be a floating point number.
Can you rerun step 4 and email me the ipyrad_log.txt(gets created in whatever directory you're in when ipyrad is run, probably your working directory on the cluster)
Robin Sleith
@R0cknRobin_twitter
Jun 02 2016 22:20
2016-05-29 15:18:37,659 pid=24600 [assembly.py] ERROR shutdown warning: array([ 0.02526304]) is not JSON serializable
2016-05-29 15:18:38,089 pid=24600 [assembly.py] ERROR Unknown format code 'f' for object of type 'unicode'
2016-05-29 15:18:38,117 pid=24600 [assembly.py] ERROR shutdown warning: array([ 0.02526304]) is not JSON serializable this is the output from the run that failed, do you want me to do step 4 all on its own or will this suffice?
Isaac Overcast
@isaacovercast
Jun 02 2016 22:23
Actually that is helpful, but still mysterious. Is that the content of the log file after running step 4?
Robin Sleith
@R0cknRobin_twitter
Jun 02 2016 22:28
Thats the log file that corresponds to the json file I sent. I will run step 4 on its own and report back