These are chat archives for dereneaton/ipyrad

Jun 2017
richie hodel
Jun 12 2017 23:49
Hi, I'm having an issue with tetrad. I ran the following command, and it worked fine:
tetrad -s Rhiman_single_6_b.snps.phy -l -n test_1 -c 8 -b 10
Then, when I tried to do another 90 bootstrap reps, I used the following command:
tetrad -j analysis-tetrad/test_1.tet.json -b 100 -c 8
and I got error messages, specifically that my .json couldn't be found:
Traceback (most recent call last):
File "/home/hodel/miniconda2/bin/tetrad", line 11, in <module>
load_entry_point('ipyrad==0.6.15', 'console_scripts', 'tetrad')()
File "/home/hodel/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/", line 192, in main
data = ipa.tetrad(, workdir=args.workdir, load=True)
File "/home/hodel/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/", line 210, in init
self._load_json(, self.dirs)
File "/home/hodel/miniconda2/lib/python2.7/site-packages/ipyrad/analysis/", line 863, in _load_json
Cannot find checkpoint (.tet.json) file at: {}""".format(path))
File "/home/hodel/miniconda2/lib/python2.7/site-packages/ipyrad/assemble/", line 51, in init
raise IPyradError(args, *kwargs)
ipyrad.assemble.util.IPyradError: Cannot find checkpoint (.tet.json) file at: /ufrc/soltis/hodel/RAD_Caribbean/Rhiman_single_6_b_outfiles/analysis-tetrad/test.tet.json