matted-zz
commented
7 years ago Thanks! This is puzzling; I'll have to look into it more closely. As a possible workaround, would you mind trying one of the previous releases (accessible here or via git clone --branch v0.10.2 https://github.com/matted/multipool.git)? From a quick glance it seems like the problem is arising in new code added after the 0.10.2 release.
jayoung
Hi there,
Thanks very much for multipool - I think it'll be really useful for us.
We have a yeast dataset we're trying to run it on. It runs fine on most chromosomes, but with three chromosomes, we get an error - I've pasted the full output below, but the last line is this: "ValueError: Unable to create correctly shaped tuple from inf". I'm guessing there's something odd about the data we have for this chromosome that's breaking multipool. Doing some plots of our own doesn't show anything very obvious yet, but we're in the early days of exploring this dataset.
I know I'm using newer versions of the dependencies than you list on the wiki page. At first I thought maybe that was the problem, so I have also tried setting up a virtual environment where I install the same versions listed on the multipool wiki page ("python 2.7.3, scipy 0.9.0, numpy 1.6.1, and matplotlib 1.1.1rc are used."). Is matplotlib 1.1.1rc the same as matplotlib 1.1.1? I'm not clear on where to get the rc version, if that's different. Anyway, using that virtual environment, I haven't managed to get mp_inference.py to run even on your test files. Again, I've pasted the full error below, but the last couple of lines look like this:
File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 66, in load_table variances = numpy.full(len(bin_starts), numpy.inf) AttributeError: 'module' object has no attribute 'full' When I google that, it seems to suggest that numpy.full function isn't in v 1.6.1 of numpy - can you clarify the package versions you're using?
I'm happy to share the data files that seem to generate this error, if you're able to take a look at them? Hope this isn't too much of a pain to deal with.
Thanks very much,
Janet Young
Dr. Janet Young
Malik lab http://research.fhcrc.org/malik/en.html
Division of Basic Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., A2-025, P.O. Box 19024, Seattle, WA 98109-1024, USA.
tel: (206) 667 4512 email: jayoung ...at... fhcrc.org
error with our default package versions:
Multipool version: 0.10.2 Python version: 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] Scipy version: 0.13.3 Numpy version: 1.8.2 Matplotlib version: 1.3.1 Recombination fraction: 0.00030303030303 in cM: 3300.0 cutoff: 497.0 Filtering allele counts: [ 359. 189.] Filtering allele counts: [ 371. 157.] Filtering allele counts: [ 260. 238.] Filtering allele counts: [ 365. 340.] Filtering allele counts: [ 293. 269.] Filtering allele counts: [ 243. 302.] Filtering allele counts: [ 400. 268.] Filtering allele counts: [ 443. 252.] Filtering allele counts: [ 564. 269.] Filtering allele counts: [ 290. 231.] Filtering allele counts: [ 220. 310.] Filtering allele counts: [ 327. 195.] Filtering allele counts: [ 320. 241.] Filtering allele counts: [ 584. 310.] Filtering allele counts: [ 261. 246.] Filtering allele counts: [ 211. 344.] Filtering allele counts: [ 268. 292.] Filtering allele counts: [ 243. 274.] Filtering allele counts: [ 271. 365.] Filtering allele counts: [ 384. 457.] cutoff: 509.0 Filtering allele counts: [ 274. 385.] Filtering allele counts: [ 217. 301.] Filtering allele counts: [ 294. 356.] Filtering allele counts: [ 309. 363.] Filtering allele counts: [ 228. 282.] Filtering allele counts: [ 316. 368.] Filtering allele counts: [ 277. 376.] Filtering allele counts: [ 263. 572.] Filtering allele counts: [ 111. 420.] Traceback (most recent call last): File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 459, in
y, y_var, y2, y_var2, d, d2, T, bins = doLoading(args.fins, args.filter)
File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 232, in doLoading
y_var = numpy.pad(y_var, pad_widths, 'constant', constant_values=numpy.inf)
File "/usr/lib/python2.7/dist-packages/numpy/lib/arraypad.py", line 1320, in pad
kwargs[i] = _normalize_shape(narray, kwargs[i])
File "/usr/lib/python2.7/dist-packages/numpy/lib/arraypad.py", line 1044, in _normalize_shape
raise ValueError(fmt % (shape,))
ValueError: Unable to create correctly shaped tuple from inf
error when I try to use virtual env
Multipool version: 0.10.2 Python version: 2.7.3 (default, Jan 21 2016, 14:53:14) [GCC 4.8.4] Scipy version: 0.9.0 Numpy version: 1.6.1 Matplotlib version: 1.1.1 Recombination fraction: 0.00030303030303 in cM: 3300.0 cutoff: 300.0 Filtering allele counts: [ 186. 128.] Filtering allele counts: [ 200. 138.] Filtering allele counts: [ 198. 187.] Filtering allele counts: [ 87. 248.] Filtering allele counts: [ 161. 163.] Filtering allele counts: [ 140. 192.] Filtering allele counts: [ 273. 55.] Filtering allele counts: [ 1083. 2086.] Filtering allele counts: [ 189. 165.] Filtering allele counts: [ 271. 92.] Filtering allele counts: [ 60. 276.] Filtering allele counts: [ 260. 207.] Filtering allele counts: [ 122. 184.] Filtering allele counts: [ 276. 59.] Filtering allele counts: [ 125. 177.] Filtering allele counts: [ 108. 240.] Filtering allele counts: [ 217. 148.] Filtering allele counts: [ 244. 147.] Filtering allele counts: [ 169. 144.] Filtering allele counts: [ 160. 142.] Filtering allele counts: [ 96. 221.] Filtering allele counts: [ 240. 218.] Filtering allele counts: [ 204. 122.] Filtering allele counts: [ 179. 172.] Filtering allele counts: [ 267. 89.] Filtering allele counts: [ 191. 161.] Filtering allele counts: [ 149. 169.] Filtering allele counts: [ 235. 112.] Filtering allele counts: [ 152. 169.] Filtering allele counts: [ 153. 157.] Filtering allele counts: [ 213. 129.] Filtering allele counts: [ 227. 118.] Filtering allele counts: [ 192. 250.] Filtering allele counts: [ 154. 165.] Filtering allele counts: [ 189. 236.] Traceback (most recent call last): File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 459, in
y, y_var, y2, y_var2, d, d2, T, bins = doLoading(args.fins, args.filter)
File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 201, in doLoading
y,y_var,d, bins = load_table(fins[0], res, False, filt)
File "/home/jayoung/malik_lab_shared/linux_gizmo/bin/mp_inference.py", line 66, in load_table
variances = numpy.full(len(bin_starts), numpy.inf)
AttributeError: 'module' object has no attribute 'full'