float error

[david-dayan]

Hi,

Any idea what might be going on here?

reading input file to obtain list of het variants
#clusters 1:13048 2:6432 3:5408 4:5766 5:6849 6:8297 7:9978 8:11394 9:12177 10:13160 11:12360 12:12177 13:11059 14:9861 15:8792 16:8089 17:7425 18:6889 19:6366 20:6041 21:5767 22:5697 23:5456 24:5074 25:4560 26:4120 27:3799 28:3292 29:2820 30:2589 31:2174 32:2025 33:1858 34:1652 35:1516 36:1407 37:1366 38:1185 39:1151 40:1072 41:1107 42:994 43:964 44:983 45:946 46:923 47:860 48:887 49:790 50:692 51:737 52:664 53:646 54:699 55:584 56:599 57:556 58:484 59:501 60:507 61:489 62:454 63:440 64:373 65:383 66:376 67:328 68:343 69:326 70:300 71:305 72:298 73:274 74:276 75:262 76:256 77:231 78:221 79:238 80:201 81:204 82:181 83:165 84:153 85:151 86:150 87:143 88:136 89:131 90:115 91:113 92:90 93:96 94:96 95:111 96:79 97:86 98:77 99:81 100:81 101:82 102:61 103:57 104:67 105:66 106:58 107:46 108:47 109:54 110:47 111:46 112:51 113:33 114:41 115:31 116:36 117:26 118:22 119:20 120:29 121:24 122:30 123:20 124:21 125:19 126:29 127:10 128:18 129:15 130:18 131:16 132:14 133:7 134:11 135:12 136:12 137:11 138:5 139:10 140:5 141:10 142:11 143:6 144:2 145:8 146:11 147:5 148:7 149:4 150:3 151:10 152:3 153:8 154:5 155:4 156:4 157:5 158:1 159:1 160:2 161:3 162:2 163:1 164:3 165:2 166:1 167:1 168:2 169:2

identified 12 het variants filtered 8151 high-cov 1e-07 0.0 0.0 0.0
processing reads for chrom groupI with 276 reads filteredreads 18646 [276, 9] 0.048913041706
processing reads for chrom groupIII with 118 reads filteredreads 28228 [394, 12] 0.0456852780283
clus2-singlechrom groupIII 1 0 0.0
clusters-2 00: 1 01: 0 f2= 0.0 A0: 1.0 dup-counts 1.0 1.0 1.0

processing reads for chrom groupIV with 25 reads filteredreads 23211 [419, 27] 0.0966587089103
processing reads for chrom groupV with 134 reads filteredreads 9589 [553, 29] 0.0786618430622
clus2-singlechrom groupV 1 0 0.0
clusters-2 00: 2 01: 0 f2= 0.0 A0: 0.5 dup-counts 2.0 2.0 1.0

processing reads for chrom groupVII with 186 reads filteredreads 31439 [739, 36] 0.0730717175498
clus2-singlechrom groupVII 1 0 0.0
clusters-2 00: 3 01: 0 f2= 0.0 A0: 0.666666666667 dup-counts 3.0 3.0 1.0

processing reads for chrom groupIX with 391 reads filteredreads 26748 [1130, 49] 0.065044247212
processing reads for chrom groupXII with 258 reads filteredreads 36167 [1388, 52] 0.056195965013
processing reads for chrom groupXIV with 279 reads filteredreads 25306 [1667, 68] 0.0611877620805
processing reads for chrom groupXVI with 176 reads filteredreads 25152 [1843, 71] 0.0577862178091
processing reads for chrom scaffold_581 with 261 reads filteredreads 75545 [2104, 79] 0.056321292508
clus2-singlechrom scaffold_581 1 0 0.0
clusters-2 00: 4 01: 0 f2= 0.0 A0: 0.5 dup-counts 4.0 4.0 1.0

AB_counts 1 3 0.25 0.75 1.25 0.75 0.5
dup-counts ignored 1 [5, 4.0, 4.0] 13048
dup-counts ignored 2 [4, 4.0, 4.0, 0.0] 6432
dup-counts ignored 3 [0, 0.0, 0.0, 0.0] 5408
dup-counts ignored 4 [1, 0.0, 0.0, 0.0, 0.0] 5766
dup-counts ignored 5 [2, 2.0, 2.0, 0.0, 0.0] 6849
dup-counts ignored 6 [2, 2.0, 2.0, 0.0, 0.0, 0.0] 8297
dup-counts ignored 7 [2, 1.0, 1.0, 0.0, 0.0, 0.0] 9978
dup-counts ignored 8 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 11394
dup-counts ignored 9 [2, 2.0, 2.0, 0.0, 0.0, 0.0, 0.0] 12177
dup-counts ignored 10 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0] 13160
dup-counts ignored 11 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 12360
dup-counts ignored 12 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 12177
dup-counts ignored 13 [3, 3.0, 3.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 11059
dup-counts ignored 14 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 9861
dup-counts ignored 15 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 8792
dup-counts ignored 16 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 8089
dup-counts ignored 17 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 7425
dup-counts ignored 18 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 6889
dup-counts ignored 19 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 6366
dup-counts ignored 20 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 6041
dup-counts ignored 21 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 5767
dup-counts ignored 22 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 5697
dup-counts ignored 23 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 5456
dup-counts ignored 24 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 5074
dup-counts ignored 25 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 4560
dup-counts ignored 26 [1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 4120
dup-counts ignored 27 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 3799
dup-counts ignored 28 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 3292
dup-counts ignored 29 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 2820
dup-counts ignored 30 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 2589
dup-counts ignored 31 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 2174
dup-counts ignored 32 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 2025
dup-counts ignored 33 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1858
dup-counts ignored 34 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1652
dup-counts ignored 35 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1516
dup-counts ignored 36 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1407
dup-counts ignored 37 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1366
dup-counts ignored 38 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1185
dup-counts ignored 39 [0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1151
dup-counts ignored 40 [1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1072
dup-counts ignored 41 [1, 1.0, 1.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0] 1107

Traceback (most recent call last):
File "estimate_PCRduprate.py", line 416, in
[Frate,Ftotal,Funique,Funiqlist] = calculate_values(duplicate_counts,cluster_counts);
File "estimate_PCRduprate.py", line 139, in calculate_values
Lambda = [1.0,float(counts_PCR[1])/counts_PCR[0]];
ZeroDivisionError: float division by zero

Thanks,
David

[vibansal]

Looks like there are very few heterozygous variants for estimating the PCR duplication rate. This leads to zero read counts and a floating point error.