These are chat archives for dereneaton/ipyrad

8th
May 2017
leclearnm
@leclearnm
May 08 2017 20:30

@dereneaton
Hi Deren, I have had a few errors running the latest version of tetrad
First, when trying to resume bootstrapping using the .json file:

export OMP_NUM_THREADS=48

ipcluster start --daemonize 
tetrad -j test.tet.json -c 48 -b 100 --ipcluster &>tetrad.log
ipcluster stop

Gives the following error:

-------------------------------------------------------
tetrad [v.0.6.19] (ipyrad.analysis toolkit)
Quartet inference from phylogenetic invariants
-------------------------------------------------------
loading seq array [57 taxa x 152900 bp]
Traceback (most recent call last):
  File "/home1/03530/nleclear/miniconda2/bin/tetrad", line 11, in <module>
    load_entry_point('ipyrad==0.6.19', 'console_scripts', 'tetrad')()
  File "/home1/03530/nleclear/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__tetrad_cli__.py", line 256, in main
    print(ipa.tetrad.LOADING_MESSAGE.format(data.name, 
AttributeError: type object 'Tetrad' has no attribute 'LOADING_MESSAGE'

Then when trying to start a fresh tetrad run with a different dataset:

ipcluster start --n=48 --profile=ipyrad --daemonize && sleep 120
tetrad -s *.snps.phy -c 48 -b 100 -n kept88m8  --ipcluster &>tetrad.log
ipcluster stop --profile=ipyrad

I received this error:

-------------------------------------------------------
tetrad [v.0.6.19] (ipyrad.analysis toolkit)
Quartet inference from phylogenetic invariants
-------------------------------------------------------
loading seq array [57 taxa x 137345 bp]
tetrad instance: kept88m8
host compute node: [48 cores] on nid00010
inferring 395010 induced quartet trees
[####################] 100%  initial tree | 0:04:10 |  

Best tree inferred from the full SNP array:
  /scratch/03530/nleclear/jatropha/ultimate/keptoutfiles/4allele/jat-kept-fw88m8_outfiles/analysis-tetrad/kept88m8.tree


  Exception found: 'TreeNode' object has no attribute 'tree'
Traceback (most recent call last):
  File "/home1/03530/nleclear/miniconda2/bin/tetrad", line 11, in <module>
    load_entry_point('ipyrad==0.6.19', 'console_scripts', 'tetrad')()
  File "/home1/03530/nleclear/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/__tetrad_cli__.py", line 261, in main
    data.run(force=args.force)
  File "/home1/03530/nleclear/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 972, in run
    self._finalize_stats(ipyclient)
  File "/home1/03530/nleclear/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/tetrad.py", line 784, in _finalize_stats
    qtre.tree.unroot()
AttributeError: 'TreeNode' object has no attribute 'tree'

It calculates the initial tree, but choke on the bootstrap

Deren Eaton
@dereneaton
May 08 2017 23:52
Hi @leclearnm, there were some major changes to tetrad recently. Including the incorporation of a new Tree object, which is what is causing this error. It is no longer compatible with the older tetrad .json files from your earlier runs, unfortunately, so you'll have to create a new object instead of loading from a .json file. I hope it's not too much inconvenience, tetrad doesn't have too many users yet so I haven't been too careful about preserving backwards compatibility. Let me know if that doesn't work, and if you run into any other bugs.