These are chat archives for dereneaton/ipyrad

Mar 2016
Isaac Overcast
Mar 02 2016 16:01
I'm considering just setting max_fragment_length for 'gbs' to be the same as 'pair', we're having so much trouble with overlapping reads I think this is the only way we can ensure it'll work w/o doing some kind of funky trimming.
Deren Eaton
Mar 02 2016 16:25
OK, I'm into it.
life is so much easier with single-end RAD data, right?
Deren Eaton
Mar 02 2016 16:56
any idea what this means:
  ipyrad [v.0.1.66]
  Interactive assembly and analysis of RADseq data
  loading Assembly: full_dentatum [/scratch/els62/Viburnum_RAD/ipyrad/dentatum/full_dentatum.json]
  ipyparallel setup: Local connection to 16 Engines

Waiting for connection file: ~/.ipython/profile_default/security/ipcontroller-ipyrad-30885-client.json
  Step3: Clustering/Mapping reads

    Skipping: All 79 selected Samples already clustered.
    (can overwrite with force argument)

    Saving Assembly.
  Step4: Joint estimation of error rate and heterozygosity
error checking 07131415-9f64-40cb-b1a1-418d350a09ce
error checking 6be59a0a-2451-4c7f-8f1d-77637306fff2
error checking 7eb70e51-9770-41cd-bd4c-b73e4c6505a5
error checking b827094b-b823-4904-83b7-72c03e0cf84d
error checking 28520d8d-481e-44a4-bbb5-ffb4e316b669
error checking 609ff5fc-587b-49b4-8ae9-f07420bf139f
error checking 6bf846a3-060a-4a7b-95a7-855a4f410379
error checking 5ce78e2d-a837-4ca5-ab95-4c391d31960b
error checking 0f67489c-36a3-41b8-83fd-a27bffa8ec77
error checking 4dcf97f8-7d19-4ccf-91b2-fba58979c88b
error checking e9a49843-6dcd-4985-8ba8-f9fe2bcecafe
error checking 71f581ef-8f68-4df4-a7f4-3890df5afd13
error checking dbfc95a0-86e2-493d-9a2a-a39748bd7dad
error checking 9976a3f1-f8ec-4558-8d45-c33c1cd35b5b
error checking 94ecbdcd-4248-401c-81fc-9fcad2ef46fa
error checking 3003f609-1727-4da4-9a5d-84daa3998b41
error checking 19a849cd-17cd-4ab5-bceb-849bf67850f4
error checking cf36d6de-58a8-4d9d-9931-110327926ea1
error checking 2434ef04-1d9f-431c-9c3b-d0256f43e1ce
error checking 21d8e66d-3126-4044-961c-2e93042e18fc
error checking 23794e74-72ce-4847-8bb0-615e8a283b19
error checking 51db9cfb-a1ec-4afd-a24d-aad6c4f9c5f3
oh, i found there is a snippet in jointestimate which prints error checking {}
Deren Eaton
Mar 02 2016 19:04
Fixed the problem. Some messed up stuff from the jobs ending in an error.
I found and fixed a bug in step6 that arises if not all samples are in state=5.
Deren Eaton
Mar 02 2016 23:17
ipyparallel 5.0.1 is now on conda! I'm gonna set ipyparallel>5.0 in requirements so that the --MPI flag will work for all updated installs
it has this annoying thing of printing to screen "Waiting for connection file: ~/.ipython/profile_default/security/ipcontroller-ipyrad-2041-client.json"
I'm gonna try to hide that during ipcluster startup