These are chat archives for dereneaton/ipyrad

Apr 2017
Apr 21 2017 01:01
hi @dereneaton @isaacovercast I got a error when i was running ipyrad this morning. I have ran ipyrad many times with same setting, only got the error this time. Could you guys help me with this? Here is the log file:
Begin run: 2017-04-21 09:51
Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 24, 'params': 'params-strumigenys_male.txt', 'branch': None, 'steps': '345', 'debug': False, 'new': None, 'MPI': True}
Platform info: ('Linux', 'sango40307', '2.6.32-431.el6.x86_64', '#1 SMP Fri Nov 22 03:15:09 UTC 2013', 'x86_64')2017-04-21 09:52:13,051 pid=10185
[] ERROR IPyradWarningExit: No ipcluster instance found. This may be a problem with your installation
setup. I would recommend that you contact the ipyrad developers.
Apr 21 2017 06:32
Hi @dereneaton and thanks for the prompt reply. It's a pity at this time there is no way of linking SNPs in the vcf to loci in the .loci file, it would very useful to be able to subsample the .loci file based on genomic information or other criteria (i.e. by chromosome, thinning etc..) and all would be needed is a list matching loci to SNPs. One could simply add the Locus number to the vcf file to the corresponding SNPs perhaps?. Just an idea!