These are chat archives for dereneaton/ipyrad

10th
Oct 2016
Edgardo M. Ortiz
@edgardomortiz
Oct 10 2016 15:57
Hello @dereneaton @isaacovercast I have some samples that don't finish clustering after 48hrs and I want to use the new -t option but I am not sure how to use it in combination with the ipclusters settings for number of engines. If the node has 48 cores, would it be ok to set ipcluster --n=12 and ipyrad -t 4 ?
Deren Eaton
@dereneaton
Oct 10 2016 16:01
You would want ipcluster start --n=48 and ipyrad ... -c 48 -t 4 --ipcluster
Edgardo M. Ortiz
@edgardomortiz
Oct 10 2016 16:01
Great! thanks
James Clugston
@Cycadales_twitter
Oct 10 2016 17:53
@dereneaton @isaacovercast Hi guys I have a problem with a large run that has been going where during step seven I get this error Encountered an unexpected error (see ./ipyrad_log.txt) Error message is below ------------------------------- "Unable to open object (Object 'seqs' doesn't exist)

@dereneaton @isaacovercast from the debug I get ```Debug results:

2016-10-10 05:51:21,350 pid=1263 [load.py] WARNING skipping: no svd results present in old assembly
2016-10-10 05:51:21,644 pid=1263 [parallel.py] INFO ['ipcluster', 'start', '--daemonize', '--cluster-id=ipyrad-1263', '--engines=MPI', '--profile=default', '--n=10', '--ip=*']
2016-10-10 05:51:32,289 pid=1263 [assembly.py] INFO "Unable to open object (Object 'seqs' doesn't exist)"
2016-10-10 05:51:32,346 pid=1263 [assembly.py] INFO shutting down engines
2016-10-10 05:51:32,433 pid=1263 [load.py] WARNING skipping: no svd results present in old assembly
2016-10-10 06:26:17,269 pid=1131 [load.py] DEBUG skipping: no svd results present in old assembly
2016-10-10 06:26:17,271 pid=1131 [load.py] WARNING
load_json found 4 keys that are unique to the older Samples.

   - assembly [Cmac] v.[0.3.42] has: set(['filtered_by_adapter', 'filtered_by_qscore', 'reads_filtered', 'reads_passed'])
   - current assembly is v.[0.3.42]

2016-10-10 06:26:17,579 pid=1131 [parallel.py] INFO ['ipcluster', 'start', '--daemonize', '--cluster-id=ipyrad-1131', '--engines=MPI', '--profile=default', '--n=40', '--ip=']
2016-10-10 06:26:28,908 pid=1131 [assembly.py] INFO "Unable to open object (Object 'seqs' doesn't exist)"
2016-10-10 06:26:28,961 pid=1131 [assembly.py] INFO shutting down engines
2016-10-10 06:26:29,040 pid=1131 [assembly.py] INFO finished shutdown
2016-10-10 06:26:29,110 pid=1131 [load.py] DEBUG skipping: no svd results present in old assembly
2016-10-10 06:29:19,882 pid=1287 [load.py] DEBUG skipping: no svd results present in old assembly
2016-10-10 06:29:20,213 pid=1287 [parallel.py] INFO ['ipcluster', 'start', '--daemonize', '--cluster-id=ipyrad-1287', '--engines=MPI', '--profile=default', '--n=40', '--ip=
']
```

@dereneaton @isaacovercast What I have done to try and correct it is update ipyrad and run it from step four. I am quite hesitant to run it from step three to be honest.
Deren Eaton
@dereneaton
Oct 10 2016 18:05
Hey @Cycadales_twitter, most of those warning in the log file are unrelated to this error (Unable to open object 'seqs'), and just indicate that some attributes of the assembly object have changed between the latest version of ipyrad and the one you used to originally create the Assembly. If you restarted from step 4 then I am surprised that you would get this error, and I don't think you should have to run step3 again.
it definitely seems to be a problem in step 6.
You are running single-end ez-rad data right?
or paired?
James Clugston
@Cycadales_twitter
Oct 10 2016 18:28
@dereneaton well I did not update ipyrad until I get the error in the first place. We are running paired ezRAD.