These are chat archives for dereneaton/ipyrad

2nd
Mar 2017
Emily Warschefsky
@ewarschefsky_twitter
Mar 02 2017 02:14
@dereneaton - I got my hands on a decent reference genome to work with (yay!) but have two questions. First, what happens if a read does not uniquely map to the reference? I don't see a parameter for this, and I can't tell what the default setting is (though I assume it discards those reads?) Second, I have a genome sequence, but I also have a file of the repetitive elements in the genome so that I can filter those out of the dataset. Can you see a way to both filter out the repetitive elements and assemble to the reference? Essentially, what I'm going for is a 5th assembly option that is +reference1 -reference2. Thanks for your input!
Isaac Overcast
@isaacovercast
Mar 02 2017 03:15
@ksil91 Ok, I definitely fixed this, it will go out with the next conda package.
joqb
@joqb
Mar 02 2017 13:50

@dereneaton @isaacovercast yesterday I was trying to follow the tutorial to get STRUCTURE running parallel that I didn't completely manage in the end, which is a pity but that's OK.

However today I am getting issues:

at first after ipyrad -p params-good_samples.txt -s 34567 -c 15

the error returned something about ipcluster so after searching a bit I found this which I tried without success
ipcluster start --n=15 --daemonize --profile=ipyrad
sleep 60
ipyrad -p params-good_samples.txt -s 34567 -c 15 --ipcluster


ipyrad [v.0.6.9]

Interactive assembly and analysis of RAD-seq data

loading Assembly: good_samples
from saved path: /data/filer-5-2/brassac/Boechera/good_samples.json

Encountered an error (see details in ./ipyrad_log.txt)
Error summary is below -------------------------------
No ipcluster instance found. This may be a problem with your installation
setup. I would recommend that you contact the ipyrad developers.

I think I screwed something up, any idea how to get it working again?

Deren Eaton
@dereneaton
Mar 02 2017 16:04
@joqb were you running the structure tutorial as a jupyter-notebook? Where did you run into a problem? I updated the HPC advice script, the part you copied above was out of date. You should exclude the "--profile=ipyrad" part of it.
joqb
@joqb
Mar 02 2017 19:28

@dereneaton I was running the tutorial outside the jupyter-notebook.
I don't exactly remember where I got stuck, it was pretty late yesterday when I tried it. However today while I was trying to repeat it I got problems with

 import pandas as pd

ValueError                                Traceback (most recent call last)
<ipython-input-8-af55e7023913> in <module>()
----> 1 import pandas as pd

/data/filer-5-2/brassac/miniconda2/lib/python2.7/site-packages/pandas/__init__.py in <module>()
     23
     24 try:
---> 25     from pandas import hashtable, tslib, lib
     26 except ImportError as e:  # pragma: no cover
     27     module = str(e).lstrip('cannot import name ')  # hack but overkill to use re

pandas/src/numpy.pxd in init pandas.lib (pandas/lib.c:85430)()

ValueError: numpy.dtype has the wrong size, try recompiling. Expected 88, got 96

although numpy loaded without error...

I tried running ipyrad without "--profile=ipyrad", it's running fine.
Thank you