search

pblischak / HyDe

Hybridization detection using phylogenetic invariants
http://hybridization-detection.readthedocs.io
GNU General Public License v3.0
41 stars 15 forks source link

segmentation fault #21

Closed rakeuler closed 3 years ago

rakeuler commented 3 years ago

I'm getting a segmentation fault error after it finishes reading the input file. I've been able to run this script with success on several other files, so I'm not sure what is causing this error now.

rakeuler commented 3 years ago

Well I was able to fix this but now I'm getting the following error: /u@/h:/w/$run_hyde.py -i goodhundredalignment.txt -m mapTwelve.txt -o out1 -n 65 -t 12 -s 354651

Running run_hyde.py

Reading input file.................................................................Done. Reading map file .................................................................Done. Traceback (most recent call last): File "/fslhome/rakeuler/miniconda3/bin/run_hyde.py", line 4, in import('pkg_resources').run_script('phyde==0.4.3', 'run_hyde.py') File "/fslhome/rakeuler/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/fslhome/rakeuler/miniconda3/lib/python3.7/site-packages/pkg_resources/init.py", line 1463, in run_script exec(code, namespace, namespace) File "/zhome/rakeuler/miniconda3/lib/python3.7/site-packages/phyde-0.4.3-py3.7-linux-x86_64.egg/EGG-INFO/scripts/run_hyde.py", line 140, in data = hd.HydeData(infile, mapfile, outgroup, nind, ntaxa, nsites, quiet, ignore_amb_sites) File "phyde/core/data.pyx", line 130, in phyde.core.data.HydeData.init KeyError: 'out1'

pblischak commented 3 years ago

Is 'out1' the name that you gave to your outgroup or is it just the name of one of the individuals in the outgroup taxon?

rakeuler commented 3 years ago

'out1' is the name I'd selected for the output file.

pblischak commented 3 years ago

Ah OK I see -- the -o flag is to specify the name of the outgroup taxon. If you want 'out1' to be the name for the output file then you can use --prefix out1

rakeuler commented 3 years ago

Thank you! This is what I get for copying parameters from old analyses rather than just reviewing documentation.

pblischak commented 3 years ago

No worries! Glad it is working