Error on running test data #94
Description
Hi,
I tried to run the program on my data which is snps from stacks pipeline but failed. So I used test data and have the same error. The whole execution is below
structure_threader run -i SmallTestData.structure -o test -t 20 -fs ~/.local/bin/fastStructure -K 1 --ind indfile.txt
INFO: Running: /home/qnick/.local/bin/fastStructure -K 1 --input /home/qnick/Downloads/strTreader_testData/SmallTestData.structure --output /home/qnick/Downloads/strTreader_testData/test/fS_run_K --format str --seed 1235813
INFO: Writing logfile for K1, replicate 1. Please wait...
INFO:
==============================
CRITICAL: 1 faststructure runs exited with errors. Check the log files of the following output files:
ERROR: /home/qnick/Downloads/strTreader_testData/test/fS_run_K
Traceback (most recent call last):
File "/home/qnick/.local/bin/structure_threader", line 8, in <module>
sys.exit(main())
File "/home/qnick/.local/lib/python3.10/site-packages/structure_threader/structure_threader.py", line 353, in main
full_run(arg)
File "/home/qnick/.local/lib/python3.10/site-packages/structure_threader/structure_threader.py", line 311, in full_run
bestk = structure_harvester(arg.outpath, wrapped_prog)
File "/home/qnick/.local/lib/python3.10/site-packages/structure_threader/structure_threader.py", line 192, in structure_harvester
bestk = sh.main(resultsdir, outdir)
File "/home/qnick/.local/lib/python3.10/site-packages/structure_threader/evanno/fastChooseK.py", line 119, in main
% Ks[np.argmax(marginal_likelihoods)]
File "/home/qnick/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 1229, in argmax
return _wrapfunc(a, 'argmax', axis=axis, out=out, **kwds)
File "/home/qnick/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 56, in _wrapfunc
return _wrapit(obj, method, *args, **kwds)
File "/home/qnick/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 45, in _wrapit
result = getattr(asarray(obj), method)(*args, **kwds)
ValueError: attempt to get argmax of an empty sequence
I'm running it on Ubuntu 22.04 with both python2 and python3 installed (thus I came across structure_threader ;) )
Is there any hope I will finally get the structure results? In desperation I started running dapc but without any information returned to the screen I don't even know if it works. Gosh I love Structure! It was so nice with msats...
Cheers,
Maciek