These are chat archives for dereneaton/ipyrad

22nd
May 2018
Katherine Silliman
@ksil91
May 22 2018 12:21

@isaacovercast @dereneaton I have been using the API in notebooks for filtering low coverage individuals. After updating to 0.7.21, it seems that the Assembly object changed a little in how it stores S7 stats. This code doesn't work anymore:

## get list of samples found in at least 40% of loci after Step 7
skeep = s3filt.stats.index[s3filt.stats_dfs.s7_samples.sample_coverage > loci40].tolist()

It gives this error:

AttributeError: No such attribute: s7_samples

Is there another way to filter samples by their S7 stats properties?

Natalia Gallego
@NataGalle_twitter
May 22 2018 15:23

@isaacovercast @dereneaton Hi guys, I hit this error while running step 3. Any thoughts on this?
[####################] 100% dereplicating | 0:02:50
[####################] 100% clustering | 5 days, 10:13:08
[####################] 100% building clusters | 0:06:06

Encountered an unexpected error (see ./ipyrad_log.txt)
Error message is below -------------------------------
KeyError('0001c1b33b9e97d776808d7022a5e107;size=59;')

Isaac Overcast
@isaacovercast
May 22 2018 15:32
Hi Natalia! Mmm, what version of ipyrad are you running? Is there anything that looks useful in the ipyrad_log.txt file?
Natalia Gallego
@NataGalle_twitter
May 22 2018 15:42
@isaacovercast v0.7.23. It says the same thing " Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': None, 'cores': 40, 'params': 'params-both2.txt', 'branch': None, 'steps': '345', 'debug': False, 'new': None, 'download': None, 'MPI': True}
Platform info: ('Linux', 'node-7-amd.local', '2.6.32-504.8.1.el6.x86_64', '#1 SMP Wed Jan 28 21:11:36 UTC 2015', 'x86_64')2018-05-22 02:05:40,366 pid=7240 [assembly.py] ERROR KeyError('0001c1b33b9e97d776808d7022a5e107;size=59;')"
Bruno de Medeiros
@brunoasm
May 22 2018 19:55
@dereneaton Thanks. I'll keep an eye open for updates regarding vcf files and will do a workaround in the meanwhile.
N-atalia
@N-atalia
May 22 2018 22:35
Hi everyone, im running STRUCTURE on jupyter notebooks but i closed it when it finished replicating for each value of K and now i cant find out how to load back the data on to the notebook to finish the anlysis, could someone help me?