These are chat archives for dereneaton/ipyrad

Jul 2017
Jul 28 2017 00:07
I find in tutotial of PE GBS of pyrad, after mered the two pair-end files to one file,change the datatype from pairend to merged,so I did it same as pyrad,but I'll follow your suggestion to change it to gbs and modify the max_shared_Hs_locus,thank you. One more,one merged reads data file and two pair-end files,which do you think better for analysis?
Deren Eaton
Jul 28 2017 00:34
I'll need to update the PE GBS tutorial, that might have been quite old, we no longer use that parameter setting.
Jul 28 2017 19:13
I am having an issue running ipyrad 0.7.2 on my campus cluster. When I submit the job it goes to the node and appears to be using the cores. It creates a folder for the fastqs as well as a tmp folder. However, no files are ever created in these folders, and progress stays at 0% after a long period of time. No error is indicated. This issue occurs with my data and the admin has the same problem trying the tutorial data. It occurs whether one or multiple nodes are used. I am able to run ipyrad successfully on a normal desktop computer. Just curious if this issue has been observed before. Thanks.
Isaac Overcast
Jul 28 2017 19:44
@jstarrett If you run with -d does it write anything interesting to the ipyrad_log.txt output file?
@JStarrett it creates the tmp-chunks- folder, but never writes to it?
Jul 28 2017 20:13

ipyrad [v.0.7.2]

Interactive assembly and analysis of RAD-seq data

Begin run: 2017-07-27 12:10
Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 20, 'params': './params-3RAD_plate3Schiz_NBV.txt', 'branch': None, 'steps': '1', 'debug': False, 'new': None, 'MPI': False}
Platform info: ('Linux', 'node047', '2.6.32-504.16.2.el6.x86_64', '#1 SMP Wed Apr 22 06:48:29 UTC 2015', 'x86_64')

Oops, above is what is written in the ipyrad_log.txt file. That text is also repeated with different Begin run time stamps. Correct, the tmp-chunks-folder is created but no files are written to it.
Isaac Overcast
Jul 28 2017 21:29
@JStarrett Can you run it again with the debug flag turned on? That should give more information: ipyrad -p params_watever.txt -s 1 -d