These are chat archives for dereneaton/ipyrad

19th
Jul 2017
Nikki Phair
@phair_nikki_twitter
Jul 19 2017 08:16
@dereneaton , I forgot to ask... Is there any way to 'subsample' a pool to simulate individuals for down stream analyses? Or will iPyRAD have to analyses the population as one sample? I hope that question makes sense...
James Clugston
@Cycadales_twitter
Jul 19 2017 22:30
@isaacovercast @dereneaton Hi guys trying to get ipyrad to run but I am running into a problem with the install. I tried the above command but no luck any ideas?
Isaac Overcast
@isaacovercast
Jul 19 2017 22:47
@Cycadales_twitter Hey james. What is the error you're seeing?
James Clugston
@Cycadales_twitter
Jul 19 2017 22:48
how Do I make it black?
James Clugston
@Cycadales_twitter
Jul 19 2017 22:53
clugston@tdobz:/data/jclugston$ cd /data/jclugston/ubuntu/Carm jclugston@tdobz:/data/jclugston/ubuntu/Carm$ ipyrad -p params-Carm.txt -s 1234567 -c 42 -f -r >& Carm_final & [2] 87807 jclugston@tdobz:/data/jclugston/ubuntu/Carm$ jobs [1]+ Stopped tail -f Carm_final [2]- Running ipyrad -p params-Carm.txt -s 1234567 -c 42 -f -r &> Carm_final & jclugston@tdobz:/data/jclugston/ubuntu/Carm$ disown -bash: warning: deleting stopped job 1 with process group 87087 [2] Exit 1 ipyrad -p params-Carm.txt -s 1234567 -c 42 -f -r &> Carm_final jclugston@tdobz:/data/jclugston/ubuntu/Carm$ jobs jclugston@tdobz:/data/jclugston/ubuntu/Carm$ tail -f Carm_final from ipyrad.assemble.util import * File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/__init__.py", line 7, in <module> from . import cluster_within File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/cluster_within.py", line 31, in <module> from refmap import * File "/home/jclugston/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/refmap.py", line 15, in <module> import pysam File "/home/jclugston/miniconda2/lib/python2.7/site-packages/pysam/__init__.py", line 5, in <module> from pysam.libchtslib import * ImportError: /home/jclugston/miniconda2/lib/././libcom_err.so.3: symbol k5_strerror_r, version krb5support_0_MIT not defined in file libkrb5support.so.0 with link time reference ^Z [1]+ Stopped tail -f Carm_final jclugston@tdobz:/data/jclugston/ubuntu/Carm$ killall jobs jobs: no process found jclugston@tdobz:/data/jclugston/ubuntu/Carm$ killall ipyrad ipyrad: no process found jclugston@tdobz:/data/jclugston/ubuntu/Carm$
@isaacovercast that is the error
Isaac Overcast
@isaacovercast
Jul 19 2017 23:07
@Cycadales_twitter if you put ``` before and after then it makes copy paste output look nice
watdo
Deren Eaton
@dereneaton
Jul 19 2017 23:09
Looks like pysam again...
You followed the bioconda reinstall instructions above and it still doesn't work?