Re: [structure-group] how to input microsatellite data

[Vikram Chhatre]

Hi Audrey,

Have you checked the user manual? It describes the data file format.

V



On Mon, Aug 13, 2012 at 4:32 AM, audrey lacroix
<lacroix...@gmail.com> wrote:
> Hi,
> A stupid beginner's question!
> I cannot input my microsatellite datas in the software. I always recieve the same error message "Bad Format in Data Structure"
> I didn't succed to get the available data on Structure website to have an example.
> Any example of a file containing the same kind of data set, or explanation will be the most welcome.
>
> I have 67 ID and 7 markers.
>
> Thank you very much
>
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[Anna Gershberg]

hey Audrey!
1. You saved the data in txt (Tab delimited) format? It's the way I work with it
2. Do you have any additional information? (Locations and etc.)
3.For diploid markers, do you do it with one or two rows?
 I add an example: 10 individuals, 9 Loci (Diploid, microsatellites) Two rows.
I attach 2 files: The data in excel and the txt file. Notice I have additional column for locations.
I hope it helps

[Aaron Aunins]

If you know how to make a Genepop File, just use the program Convert
(Glaubitz 2004) to make the input file for you.

HTH - Aaron

--
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Life Sciences Building, Rm 327
1000 West Cary St
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Office Phone: 804-828-0906

[Tereza]

Hey, is there any chance you're using OSX? Structure only reads my input files when I use a .txt exported from a PC...

2012/8/13 Vikram Chhatre <cryptic...@gmail.com>

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13506-900

[Anna Gershberg]

Me? Windows

[Vikram Chhatre]

I replicated first few lines of your file to show the correct formatting:

1 2 3 4 5 6 7 8 9 10 11 12 13
1 1 179 179 220 220 244 244 310 310 178 178 246 246
187 187 -9 -9 186 186 248 248 186 186 135 135 -9 -9
2 1 193 193 232 232 242 242 316 316 174 174 255 255
164 164 203 203 218 218 250 250 192 192 147 147 208 208
3 1 205 205 212 212 242 242 326 326 178 178 255 255
168 168 203 203 216 216 250 250 192 192 147 147 124 124


Thus, you don't need to repeat the locus names twice, just because the
data is in ONEROWPERIND format. Make sure this parameter is properly
assigned in the settings dialogue box.

HTH
V





On Sat, Sep 1, 2012 at 3:04 AM, Theresa <theres...@gmail.com> wrote:
> Hi Vikram,
>
> I have exactly the same problem as Audrey's and it drives me crazy!
> I read all the comments on this group but still couln't fix mine.
> Would you help me with my data if you can? My data is copied below.
> Thanks.
>
> Theresa
>
> 77 individuals(label) one phenotype(host) 13 loci data in one row
> LabelHost 1 1 2 2 3 3 4 4 5 5 6 6 7 7 8 8 9 9 10 10 11 11 12 12 13 13
> 1 1 179 179 220 220 244 244 310 310 178 178 246 246 187 187 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 2 1 193 193 232 232 242 242 316 316 174 174 255 255 164 164 203 203 218 218 250 250 192 192 147 147 208 208
> 3 1 205 205 212 212 242 242 326 326 178 178 255 255 168 168 203 203 216 216 250 250 192 192 147 147 124 124
> 4 1 205 205 232 232 242 242 336 336 176 176 255 255 170 170 193 193 218 218 250 250 192 192 297 297 131 131
> 5 1 209 209 232 232 242 242 302 302 178 178 255 255 164 164 203 203 220 220 250 250 192 192 144 144 165 165
> 6 1 207 207 230 230 242 242 302 302 178 178 255 255 176 176 203 203 220 220 250 250 194 194 132 132 131 131
> 7 1 209 209 230 230 242 242 334 334 214 214 255 255 168 168 193 193 220 220 250 250 192 192 144 144 147 147
> 8 1 209 209 232 232 242 242 300 300 174 174 255 255 166 166 193 193 218 218 250 250 192 192 132 132 140 140
> 9 1 209 209 244 244 252 252 336 336 176 176 251 251 170 170 201 201 218 218 250 250 194 194 144 144 197 197
> 10 1 179 179 220 220 250 250 310 310 178 178 242 242 181 181 -9 -9 186 186 286 286 186 186 138 138 -9 -9
> 11 1 207 207 230 230 242 242 336 336 178 178 255 255 168 168 193 193 220 220 250 250 192 192 144 144 196 196
> 12 1 203 203 230 230 230 230 318 318 222 222 253 253 178 178 195 195 198 198 256 256 188 188 138 138 139 139
> 13 1 179 179 220 220 236 236 310 310 178 178 240 240 163 163 -9 -9 186 186 246 246 186 186 138 138 -9 -9
> 14 1 209 209 244 244 252 252 336 336 176 176 251 251 170 170 201 201 220 220 250 250 198 198 144 144 199 199
> 15 1 179 179 226 226 246 246 310 310 178 178 242 242 181 181 -9 -9 186 186 248 248 186 186 159 159 -9 -9
> 16 1 209 209 212 212 252 252 316 316 178 178 255 255 168 168 207 207 218 218 250 250 194 194 147 147 142 142
> 17 1 179 179 220 220 238 238 314 314 178 178 242 242 181 181 -9 -9 186 186 248 248 186 186 138 138 -9 -9
> 18 1 209 209 234 234 242 242 316 316 176 176 255 255 170 170 203 203 220 220 250 250 194 194 132 132 140 140
> 19 1 207 207 234 234 242 242 334 334 176 176 257 257 164 164 193 193 252 252 300 300 192 192 300 300 249 249
> 20 1 179 179 220 220 236 236 310 310 178 178 242 242 179 179 -9 -9 186 186 246 246 186 186 138 138 -9 -9
> 21 1 179 179 218 218 246 246 306 306 178 178 240 240 181 181 -9 -9 186 186 280 280 186 186 138 138 -9 -9
> 22 1 209 209 232 232 242 242 300 300 174 174 255 255 166 166 193 193 218 218 250 250 192 192 297 297 140 140
> 23 1 209 209 232 232 242 242 336 336 178 178 255 255 168 168 191 191 220 220 250 250 192 192 144 144 142 142
> 24 1 179 179 220 220 248 248 310 310 178 178 242 242 181 181 -9 -9 186 186 250 250 186 186 132 132 -9 -9
> 25 1 207 207 212 212 252 252 316 316 178 178 255 255 168 168 207 207 218 218 250 250 194 194 147 147 140 140
> 26 2 179 179 220 220 252 252 312 312 178 178 240 240 181 181 -9 -9 186 186 250 250 186 186 132 132 -9 -9
> 27 2 179 179 220 220 236 236 310 310 178 178 240 240 181 181 -9 -9 186 186 246 246 186 186 132 132 -9 -9
> 28 2 179 179 220 220 240 240 310 310 178 178 242 242 181 181 -9 -9 186 186 252 252 186 186 135 135 -9 -9
> 29 2 179 179 220 220 246 246 314 314 176 176 255 255 170 170 203 203 224 224 250 250 192 192 144 144 147 147
> 30 2 179 179 220 220 250 250 312 312 178 178 240 240 183 183 -9 -9 186 186 254 254 186 186 132 132 -9 -9
> 31 2 179 179 220 220 248 248 312 312 178 178 240 240 183 183 -9 -9 186 186 248 248 186 186 132 132 -9 -9
> 32 2 203 203 220 220 234 234 314 314 218 218 255 255 164 164 197 197 194 194 238 238 188 188 132 132 185 185
> 33 2 179 179 226 226 266 266 312 312 178 178 240 240 171 171 -9 -9 186 186 244 244 186 186 138 138 -9 -9
> 34 2 179 179 222 222 236 236 310 310 178 178 240 240 181 181 -9 -9 186 186 246 246 186 186 138 138 -9 -9
> 35 2 179 179 220 220 244 244 312 312 178 178 240 240 185 185 -9 -9 186 186 248 248 186 186 138 138 -9 -9
> 36 2 179 179 222 222 250 250 310 310 178 178 240 240 185 185 -9 -9 186 186 282 282 186 186 135 135 -9 -9
> 37 2 179 179 220 220 272 272 312 312 178 178 240 240 183 183 -9 -9 186 186 250 250 186 186 138 138 -9 -9
> 38 2 179 179 220 220 236 236 314 314 178 178 240 240 229 229 -9 -9 186 186 246 246 186 186 132 132 -9 -9
> 39 2 179 179 218 218 236 236 310 310 178 178 240 240 163 163 -9 -9 186 186 246 246 186 186 141 141 -9 -9
> 40 2 179 179 220 220 244 244 310 310 178 178 246 246 181 181 -9 -9 186 186 244 244 186 186 144 144 -9 -9
> 41 2 205 205 230 230 242 242 332 332 216 216 255 255 170 170 207 207 220 220 250 250 196 196 297 297 209 209
> 42 2 179 179 220 220 244 244 312 312 178 178 242 242 183 183 -9 -9 186 186 246 246 186 186 141 141 -9 -9
> 43 2 179 173 222 222 234 234 312 312 178 178 240 240 183 183 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 44 2 179 179 218 218 244 244 310 310 178 178 240 240 181 181 -9 -9 186 186 248 248 186 186 132 132 -9 -9
> 45 2 179 179 218 218 236 236 310 310 178 178 242 242 163 163 -9 -9 186 186 246 246 186 186 135 135 -9 -9
> 46 2 179 173 220 220 236 236 312 312 178 178 240 240 181 181 -9 -9 186 186 248 248 186 186 200 200 -9 -9
> 47 2 179 179 216 216 236 236 306 306 178 178 240 240 163 163 -9 -9 186 186 246 246 186 186 141 141 -9 -9
> 48 2 179 179 222 222 238 238 314 314 178 178 246 246 181 181 -9 -9 186 186 248 248 186 186 141 141 -9 -9
> 49 2 179 173 220 220 236 236 312 312 178 178 240 240 183 183 -9 -9 186 186 250 250 186 186 138 138 -9 -9
> 50 2 179 179 222 222 246 246 312 312 178 178 240 240 181 181 -9 -9 186 186 242 242 186 186 153 153 -9 -9
> 51 2 179 179 220 220 248 248 312 312 178 178 240 240 181 181 -9 -9 186 186 244 244 186 186 135 135 -9 -9
> 52 2 179 179 222 222 248 248 310 310 178 178 240 240 219 219 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 53 2 179 179 220 220 244 244 312 312 178 178 242 242 183 183 -9 -9 186 186 242 242 186 186 135 135 -9 -9
> 54 2 179 179 220 220 250 250 310 310 178 178 242 242 181 181 -9 -9 186 186 252 252 186 186 135 135 -9 -9
> 55 2 179 179 218 218 236 236 312 312 178 178 242 242 183 183 -9 -9 186 186 242 242 186 186 153 153 -9 -9
> 56 2 179 179 218 218 240 240 312 312 178 178 240 240 229 229 -9 -9 186 186 248 248 186 186 141 141 -9 -9
> 57 2 179 179 220 220 236 236 312 312 178 178 240 240 183 183 -9 -9 186 186 246 246 186 186 135 135 -9 -9
> 58 2 179 179 220 220 240 240 310 310 178 178 240 240 181 181 -9 -9 186 186 248 248 188 188 135 135 -9 -9
> 59 2 179 179 218 218 248 248 320 320 178 178 246 246 181 181 -9 -9 186 186 284 284 186 186 138 138 -9 -9
> 60 2 179 179 216 216 246 246 314 314 178 178 240 240 183 183 -9 -9 186 186 244 244 186 186 132 132 -9 -9
> 61 2 193 193 212 212 244 244 316 316 178 178 255 255 168 168 201 201 218 218 250 250 194 194 147 147 214 214
> 62 2 207 207 234 234 242 242 338 338 176 176 255 255 170 170 203 203 224 224 250 250 192 192 144 144 148 148
> 63 2 179 179 220 220 244 244 312 312 178 178 240 240 189 189 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 64 2 211 211 230 230 244 244 336 336 178 178 255 255 170 170 193 193 216 216 250 250 192 192 144 144 232 232
> 65 2 179 179 226 226 266 266 312 312 178 178 240 240 163 163 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 66 2 179 179 218 218 238 238 310 310 178 178 240 240 163 163 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 67 2 179 179 218 218 236 236 310 310 178 178 240 240 161 161 -9 -9 186 186 246 246 186 186 141 141 -9 -9
> 68 2 179 179 222 222 248 248 310 310 178 178 242 242 239 239 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 69 2 193 193 212 212 244 244 316 316 178 178 253 253 168 168 199 199 218 218 250 250 194 194 147 147 215 215
> 70 2 179 179 220 220 236 236 308 308 178 178 240 240 181 181 -9 -9 186 186 242 242 186 186 153 153 -9 -9
> 71 2 179 179 218 218 238 238 312 312 178 178 242 242 181 181 -9 -9 186 186 248 248 186 186 138 138 -9 -9
> 72 2 179 179 218 218 236 236 312 312 178 178 242 242 181 181 -9 -9 186 186 246 246 186 186 135 135 -9 -9
> 73 2 179 173 218 218 244 244 308 308 178 178 240 240 181 181 -9 -9 186 186 250 250 186 186 138 138 -9 -9
> 74 2 179 179 218 218 244 244 310 310 178 178 246 246 181 181 -9 -9 186 186 248 248 186 186 135 135 -9 -9
> 75 2 209 209 234 234 242 242 338 338 176 176 253 253 170 170 201 201 224 224 250 250 192 192 144 144 148 148
> 76 2 179 179 218 218 218 276 308 308 178 178 238 238 183 183 -9 -9 186 186 252 252 186 186 135 135 -9 -9
> 77 2 211 211 230 230 244 244 336 336 178 178 253 253 170 170 191 191 216 216 250 250 192 192 144 144 234 234

>
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[Theresa]

Hi Vikram,

 

I deleted label and host and it worked!

Thank you so much.

I hope troubleshooting section is added to the documentation next time.

 

Theresa

2012년 9월 2일 일요일 오전 1시 0분 21초 UTC+9, Vikram Chhatre 님의 말:

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[Laelia Pinto]

Hi,

I have the same problem, my input files aren´t accept in STRUCTURE 2.3.4.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
AP0021208-1 1 396 400 17 19 12 12 8 12 -9 -9 129 129 489 489 218 218 19 23 17 18 -9 -9 316 356 366 366 -9 -9 11 11 400 404 20 262 7 93
AP0021208-19 1 392 404 17 18 11 13 12 13 -9 -9 125 129 485 489 210 222 17 23 15 17 -9 -9 320 320 370 370 -9 -9 11 11 408 412 19 212 9 93
AP0028108-1 1 420 396 18 17 11 14 12 13 -9 -9 121 117 493 497 214 218 22 18 15 15 -9 -9 344 348 366 366 -9 -9 10 11 400 412 20 262 7 8
AP0075308-19 1 404 412 17 20 11 10 9 11 -9 -9 125 129 497 489 214 218 19 22 16 18 -9 -9 320 316 358 358 12 13 8 10 400 404 20 242 -9 -9
AP0099708-1 1 404 404 20 22 13 14 11 13 -9 -9 129 137 485 485 214 218 22 18 17 15 -9 -9 312 340 374 358 12 12 8 12 396 416 -9 -9 7 9

These are my lines and rows.

Thanks,

[Ramesh krishnan Ramasamy]

Hi,

Please don't copy paste here, can you attach your sample file? and tell what error you are getting?

Best

Ramesh

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[Guelor Mayonde]

Hi Laelia,

Another alternative can be to use a program called "CONVERT" to help you convert your SSR data into structure format. 

I hope that helps :)

Kind Regards

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Cell: +27 71 76 26 140

[LP]

Hi,

I attach my file and the error is"Bad format in data source. Expect 18 data entires line 1".

Thanks.

LP

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[LP]

Hi,

I used "CONVERT" but the STRUCTURE show me the same error mensage.

Regards,

Laélia (Lp)

Em quarta-feira, 30 de julho de 2014 05h59min53s UTC-3, Guelor escreveu:

Hi Laelia,

Another alternative can be to use a program called "CONVERT" to help you convert your SSR data into structure format. 

I hope that helps :)

Kind Regards

On 29 July 2014 18:11, Ramesh krishnan Ramasamy <rame...@gmail.com> wrote:

Hi,

Please don't copy paste here, can you attach your sample file? and tell what error you are getting?

Best

Ramesh

On Wed, Jul 30, 2014 at 5:53 AM, Laelia Pinto <laelia...@gmail.com> wrote:

Hi,

I have the same problem, my input files aren´t accept in STRUCTURE 2.3.4.

                1               2               3               4               5               6               7               8               9               10              11              12              13              14              15              16              17              18
AP0021208-1     1       396     400     17      19      12      12      8       12      -9      -9      129     129     489     489     218     218     19      23      17      18      -9      -9      316     356     366     366     -9      -9      11      11      400     404     20      262     7       93
AP0021208-19    1       392     404     17      18      11      13      12      13      -9      -9      125     129     485     489     210     222     17      23      15      17      -9      -9      320     320     370     370     -9      -9      11      11      408     412     19      212     9       93
AP0028108-1     1       420     396     18      17      11      14      12      13      -9      -9      121     117     493     497     214     218     22      18      15      15      -9      -9      344     348     366     366     -9      -9      10      11      400     412     20      262     7       8
AP0075308-19    1       404     412     17      20      11      10      9       11      -9      -9      125     129     497     489     214     218     19      22      16      18      -9      -9      320     316     358     358     12      13      8       10      400     404     20      242     -9      -9
AP0099708-1     1       404     404     20      22      13      14      11      13      -9      -9      129     137     485     485     214     218     22      18      17      15      -9      -9      312     340     374     358     12      12      8       12      396     416     -9      -9      7       9

These are my lines and rows.

Thanks,

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[zeamne T]

Hi Laelia,

I cannot open our input file in notepad++, it seems to be a weird format. My structure files usually can be opened in notepad++. How did you get this file? From CONVERT? Maybe you can upload the file that you input into CONVERT?

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[Ramesh krishnan Ramasamy]

Yes, I also couldn't able to open, can you share simple text file?

[Rogério MG]

Hello guys. sorry for reative this topic, but I have some doubts about this and I haven't found the answer nowhere.

I use windows. I noticed everyone who prepare their microsatellite files use the pb-long (170, 176, 186, etc). But, I noticed the "Simulated microsatellite test data.txt" in the Structure website uses numbers from -7 to 10 more or less.

But it's ok, I didn't worry about this. I ran the file and it worked. Then, I used CLUMPP and it's running since two days ago and don't finished! Because of this, I would like to ask: I need to prepare the input in "pb-long" or in sequential numbers? What this sequential number in the model means? Why CLUMPP would be so slowly?

Thanks :)

[Vikram Chhatre]

You are likely using the FULLSEARCH algorithm in CLUMPP which will take a very long time.  Try with LargeKGreedy, which is option#2.

V

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[Rogério MG]

Ok. Thanks! I'll try this now.

On Sunday, June 21, 2015 at 7:52:33 PM UTC-3, Vikram Chhatre wrote:

You are likely using the FULLSEARCH algorithm in CLUMPP which will take a very long time.  Try with LargeKGreedy, which is option#2.

V

On Sun, Jun 21, 2015 at 6:50 PM, 'Rogério MG' via structure-software <structure...@googlegroups.com> wrote:

Em segunda-feira, 13 de agosto de 2012 12:47:46 UTC-3, Vikram Chhatre  escreveu:
> Hi Audrey,
>
> Have you checked the user manual?  It describes the data file format.
>
> V
>
>
>
> On Mon, Aug 13, 2012 at 4:32 AM, audrey lacroix
> <lacroix...@gmail.com> wrote:
> > Hi,
> > A stupid beginner's question!
> > I cannot input my microsatellite datas in the software. I always recieve the same error message "Bad Format in Data Structure"
> > I didn't succed to get the available data on Structure website to have an example.
> > Any example of a file containing the same kind of data set, or explanation will be the most welcome.
> >
> > I have 67 ID and 7 markers.
> >
> > Thank you very much
> >
> > --
> > You received this message because you are subscribed to the Google Groups "structure-software" group.
> > To view this discussion on the web visit https://groups.google.com/d/msg/structure-software/-/5MxOuZ088b0J.
> > To post to this group, send email to structure...@googlegroups.com.

> > To unsubscribe from this group, send email to structure-software+unsub...@googlegroups.com.

> > For more options, visit this group at http://groups.google.com/group/structure-software?hl=en.
> >

Hello guys. sorry for reative this topic, but I have some doubts about this and I haven't found the answer nowhere.

I use windows. I noticed everyone who prepare their microsatellite files use the pb-long (170, 176, 186, etc). But, I noticed the "Simulated microsatellite test data.txt" in the Structure website uses numbers from -7 to 10 more or less.

But it's ok, I didn't worry about this. I ran the file and it worked. Then, I used CLUMPP and it's running since two days ago and don't finished! Because of this, I would like to ask: I need to prepare the input in "pb-long" or in sequential numbers? What this sequential number in the model means? Why CLUMPP would be so slowly?

Thanks :)

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[Rogério MG]

Sorry for the late, but now it's working correctly!! Thanks! :)

Em domingo, 21 de junho de 2015 19:52:33 UTC-3, Vikram Chhatre escreveu:

You are likely using the FULLSEARCH algorithm in CLUMPP which will take a very long time.  Try with LargeKGreedy, which is option#2.

V

On Sun, Jun 21, 2015 at 6:50 PM, 'Rogério MG' via structure-software <structure...@googlegroups.com> wrote:

Em segunda-feira, 13 de agosto de 2012 12:47:46 UTC-3, Vikram Chhatre  escreveu:
> Hi Audrey,
>
> Have you checked the user manual?  It describes the data file format.
>
> V
>
>
>
> On Mon, Aug 13, 2012 at 4:32 AM, audrey lacroix
> <lacroix...@gmail.com> wrote:
> > Hi,
> > A stupid beginner's question!
> > I cannot input my microsatellite datas in the software. I always recieve the same error message "Bad Format in Data Structure"
> > I didn't succed to get the available data on Structure website to have an example.
> > Any example of a file containing the same kind of data set, or explanation will be the most welcome.
> >
> > I have 67 ID and 7 markers.
> >
> > Thank you very much
> >
> > --
> > You received this message because you are subscribed to the Google Groups "structure-software" group.
> > To view this discussion on the web visit https://groups.google.com/d/msg/structure-software/-/5MxOuZ088b0J.
> > To post to this group, send email to structure...@googlegroups.com.

> > To unsubscribe from this group, send email to structure-software+unsub...@googlegroups.com.

> > For more options, visit this group at http://groups.google.com/group/structure-software?hl=en.
> >

Hello guys. sorry for reative this topic, but I have some doubts about this and I haven't found the answer nowhere.

I use windows. I noticed everyone who prepare their microsatellite files use the pb-long (170, 176, 186, etc). But, I noticed the "Simulated microsatellite test data.txt" in the Structure website uses numbers from -7 to 10 more or less.

But it's ok, I didn't worry about this. I ran the file and it worked. Then, I used CLUMPP and it's running since two days ago and don't finished! Because of this, I would like to ask: I need to prepare the input in "pb-long" or in sequential numbers? What this sequential number in the model means? Why CLUMPP would be so slowly?

Thanks :)

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[Biyce]

 Hi, Vikram,

I have SSR data, i don't have problem with input data. It is running in the structure but not giving output data, it doesnt give simulation summarry. I checked tutorial and do everything but i couldnt solve the problem. my input file is attached. Thank you for your kind assistance.

On Mon, Aug 13, 2012 at 4:32 AM, audrey lacroix
<lacroix...@gmail.com> wrote:
> Hi,
> A stupid beginner's question!
> I cannot input my microsatellite datas in the software. I always recieve the same error message "Bad Format in Data Structure"
> I didn't succed to get the available data on Structure website to have an example.
> Any example of a file containing the same kind of data set, or explanation will be the most welcome.
>
> I have 67 ID and 7 markers.
>
> Thank you very much
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