Error while using groopm core

[mchaib]

Hello,
I have successfully created a database using groopm parse using my contigs and the mapped raw reads. Then, I tried using groopm core, but at some point I get an error. See below. Could you please indicate what the problem may be?
Thank you!

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[[GroopM 0.3.4]] Running in core creation mode...

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Loading data from: database.gm
GroopM DB version (5) up to date
Loaded indices with condition: length >= 1500
Working with: 156422 contigs
Loading coverage profiles
Loading PCA kmer sigs (43 dimensional space)
Loading PCA kmer variance (total variance: 0.80)
Loading contig names
Loading contig lengths (Total: 522276132 BP)
Loading contig GC ratios (Average GC: 0.586)
Creating color map
{ THIS: 0:01:55.423 || TOTAL: 0:01:55.436 }
Loading transformed data
Reticulating splines
{ THIS: 0:00:17.960 || TOTAL: 0:02:13.396 }
Create cores
.... .... .... .... .... .... .... .... .... ....
0 3461 74 356 3060 15311 1826 10 18 82 6896
10 35 198 43 20 25 74 13 58 2563 74
20 649 346 1210 1762 1507 12 1271 8 1089 1329
30 100 2313 22 207 28 667 2179 7 1563 398
40 1344 1440 1123 8 59 1437 62 186 1264 42
50 2211 1237 580 2540 59 2748 788 431 3 22
60 12 130 3576 306 36 80 38 747 3532 2083
70 1589 21 645 31 1099 7 21 12 273 4
80 1631 2898 11 186 166 191 664 416 28 1087
90 603 1209 1215 469 550 597 1492 1334 57 815
100 464 24 1015 11 64 8 149 103 294 712
110 26 1095 987 1151 81 1813 606 9 1347 64
120 276 494 1320 657 74 690 123 148 76 178
130 766 560 977 570 439 756 189 663 452 16
140 368 160 15 89 669 182 725 180 87 431
150 211 101 292 212 290 63 103 61 94 330
160 963 46 28 563 94 910 396 175 749 218
170 244 102 4 112 132 343 43 679 75 39
180 486 487 267 697 13 165 85 94 61 142
190 112 18 49 109 40 200 334 102 25 90
200 58 96 303 316 101 82 221 28 43 281
210 430 32 43 76 273 100 176 473 436 298
220 308 174 391 247 35 134 87 72 175 21
230 155 253 117 29 350 148 155 73 34 46
240 95 97 92 31 230 43 246 95 58 27
250 82 129 63 211 90 125 55 581 56 27
260 135 10 283 15 27 62 130 71 94 101
270 50 177 33 81 59 53 83 49 49 46
280 103 121 17 39 223 177 104 182 153 58
290 94 40 49 202 15 128 87 12 49 76
300 233 40 171 297 200 48 25 54 185 229
310 40 19 15 47 23 36 17 26 46 121
320 180 71 51 97 146 26 7 107 104 82
330 29 60 73 79 58 284 11 55 66 19
340 66 34 15 96 67 23 70 86 70 94
350 25 38 49 79 21 54 11 90 26 60
360 154 62 54 230
.... .... .... .... .... .... .... .... .... ....
{ THIS: 4:35:07.126 || TOTAL: 4:37:20.523 }
Refine cores [begin: 364]
Start automatic bin refinement
149801 contigs across 364 cores ( 95.77 % )
Identifying possible chimeric bins
Identified 13 likely chimeric bin(s), removed 4 small chimeric bin(s)
307,317,327,346
{ THIS: 0:00:00.818 || TOTAL: 4:37:21.341 }
Merging similar bins (351) with kCut 39.33 (+/-4.972) cCut 0.23 (+/-0.115)
Unexpected error: <type 'exceptions.FloatingPointError'>
Traceback (most recent call last):
File "/home/p270270/.local/bin/groopm", line 381, in
GM_parser.parseOptions(args)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/groopm.py", line 138, in parseOptions
gf=gf)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/cluster.py", line 217, in makeCores
self.RE.refineBins(self.timer, auto=True, saveBins=False, plotFinal=prfx, gf=gf)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/refine.py", line 158, in refineBins
graph = self.autoRefineBins(timer, makeGraph=gf!="")
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/refine.py", line 474, in autoRefineBins
self.mergeSimilarBins(graph=graph, verbose=False)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/refine.py", line 571, in mergeSimilarBins
mergers = self.findMergeGroups(kCutMedian, kCutStd, cCutMedian, cCutStd, verbose=verbose)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/refine.py", line 631, in findMergeGroups
retA=True)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/bin.py", line 352, in getBoundingKEllipseArea
(A, center, radii, _rotation) = ET.getMinVolEllipse(KPCAs, retA=True)
File "/home/p270270/.local/lib/python2.7/site-packages/groopm/ellipsoid.py", line 153, in getMinVolEllipse
radii = 1.0/np.sqrt(s)
FloatingPointError: divide by zero encountered in divide

[timbalam]

Hi mchaib,
Thanks for opening the issue. This looks like a bug possibly triggered by a bin with no or a single member contig. Shouldn't be too hard to fix. I will try to get to it before the end of the week.
Regards,
Tim

[mchaib]

Dear Tim,
Thanks for your reply. I was wondering whether you had made any progress regarding the bug? Thanks again.
Maryam

[timbalam]

Hi Maryam,

I have written a patch that should stop the crash you saw. Hopefully it
will soon be pushed to the Ecogenomics github repository. Are you able
to build from that? Unfortunately we have had issues updating the GroopM
pip repository in the past if you are using that.

I'll let you know when the patch is merged into the Ecogenomics repository.

Let me know if you run into more issues!

Regards,
Tim

On 3/02/2016 6:14 PM, mchaib wrote:

Dear Tim,
Thanks for your reply. I was wondering whether you had made any progress
regarding the bug? Thanks again.
Maryam

—
Reply to this email directly or view it on GitHub
#19 (comment).

[mchaib]

Dear Tim,

Sounds good. Sure, just let me know when it is out. I should be able to take it from there.
Many thanks,
Maryam

[jvollme]

Hello,
I recently ran into the exact same problem (using GroopM v0.3.4 installed via pip).
Has this issue already been fixed in the github repository?
Do you have instructions for building groopM from the repository instead of pip?

Edit:
it seems that the version in this repository is older than the pip-version (pip: 0.3.4, repository: 0.2.11)? Is this correct? Should I be using the older version?