These are chat archives for dereneaton/ipyrad

13th
Jun 2017
Deren Eaton
@dereneaton
Jun 13 2017 00:36
Hi @richiehodel_twitter , thanks for reporting, I'll look into it. I made some changes recently that might have broken the -j option temporarily.
Deren Eaton
@dereneaton
Jun 13 2017 20:55
@LinaValencia85 yes, I started to implement something like that but never quite finished. We'll add it to the TODO list.
@LinaValencia85 Also, very stringent adapter filtering should help with that problem.
rtm79
@rtm79
Jun 13 2017 22:16
@dereneaton @isaacovercast
@rtm79 Hi,

I'm having some trouble with the json file not being decoded when trying to run step 6. Everything up to this point has worked fine (I've been running the program step by step). I looked back through old posts and saw something about using -f, but this didn't work for me. Here's the output when using -d "-------------------------------------------------------------
ipyrad [v.0.6.17]

Interactive assembly and analysis of RAD-seq data

Begin run: 2017-06-12 21:13
Using args {'preview': False, 'force': False, 'threads': 2, 'results': False, 'quiet': False, 'merge': None, 'ipcluster': False, 'cores': 32, 'params': 'params.txt', 'branch': None, 'steps': '6', 'debug': True, 'new': None, 'MPI': True}
Platform info: ('Linux', 'nyx7015.arc-ts.umich.edu', '3.10.0-327.36.3.el7.x86_64', '#1 SMP Mon Oct 24 16:09:20 UTC 2016', 'x86_64')2017-06-12 21:13:03,434 pid=53094 [load.py] DEBUG skipping: no svd results present in old assembly
2017-06-12 21:13:11,877 pid=53094 [parallel.py] INFO ['ipcluster', 'start', '--daemonize', '--cluster-id=ipyrad-cli-23672573.nyx.arc-ts.umich.edu', '--engines=MPI', '--profile=ipyrad_arcts', '--n=32', '--ip=*']
2017-06-12 21:13:20,253 pid=53094 [assembly.py] ERROR No JSON object could be decoded

Any ideas?