error in input file

[Karen]

I am having trouble getting IMa2 to run.  I get the error message "Invalid input file: gene name - locus (0) 1-th gene name, partial name".

I don't think the error is actually the gene name, since I've used the same gene name in other input files that have worked.  Possibly it's something on a line preceding this.  I've pasted the first few lines, up to the end of the first locus below.  If anyone can explain my problem, it would be much appreciated.

Boab microsatellites
2
Coastal Inland
(0,1):2
6
Ad06          140 286       1 S1             1 0.00002 (0.00001, 0.00003)
JP62          73
JP63          73
JP64          73
JP66          73
JP67          73
JP69          73
JP70          69
JP221         73
JP222         72
JP223         76
JP224         73
JP225         73
JP226         73
JP227         73
JP228         73
JP229         73
JP230         73
JP231         82
JP232         73
JP233         73
JP234         73
JP235         73
JP236         73
JP237         73
JP238         73
JP239         77
JP240         75
JP241         83
JP242         73
JP243         73
JP244         73
JP245         72
JP246         73
JP100         73
JP101         73
JP102         73
JP104         73
JP105         74
JP107         73
JP108         74
JP109         74
JP110         73
JP111         73
JP216         75
JP217         74
JP218         73
JP219         82
JP220         82
JP71          73
JP73          73
JP75          73
JP76          73
JP77          73
JP78          73
JP79          73
JP80          69
JP81          73
JP82          69
JP84          73
JP85          84
JP90          74
JP91          73
JP92          73
JP93          69
JP94          69
JP95          73
JP96          73
JP97          73
JP98          73
JP99          77
JP62a         80
JP63a         73
JP64a         73
JP66a         73
JP67a         73
JP69a         74
JP70a         73
JP221a        77
JP222a        73
JP223a        78
JP224a        82
JP225a        73
JP226a        74
JP227a        73
JP228a        73
JP229a        80
JP230a        84
JP231a        82
JP232a        74
JP233a        74
JP234a        73
JP235a        78
JP236a        73
JP237a        73
JP238a        75
JP239a        78
JP240a        78
JP241a        83
JP242a        84
JP243a        74
JP244a        73
JP245a        73
JP246a        73
JP100a        75
JP101a        73
JP102a        74
JP104a        73
JP105a        74
JP107a        81
JP108a        81
JP109a        81
JP110a        73
JP111a        74
JP216a        81
JP217a        82
JP218a        73
JP219a        82
JP220a        85
JP71a         73
JP73a         83
JP75a         82
JP76a         73
JP77a         73
JP78a         83
JP79a         82
JP80a         82
JP81a         82
JP82a         73
JP84a         89
JP85a         89
JP90a         82
JP91a         82
JP92a         73
JP93a         69
JP94a         73
JP95a         73
JP96a         73
JP97a         83
JP98a         73
JP99a         85
JP121         73
JP122         73
JP123         73
JP124         73
JP125         73
JP126         77
JP127         73
JP128         73
JP129         73
JP130         73
JP131         73
JP132         80
JP133         80
JP134         73
JP135         73
JP136         76
JP137         73
JP138         73
JP139         73
JP140         73
JP141         83
JP142         73
JP143         72
JP144         73
JP145         82
JP146         73
JP147         72
JP148         82
JP149         72
JP150         85
JP151         74
JP152         73
JP153         73
JP154         80
JP155         73
JP156         76
JP157         76
JP158         72
JP159         73
JP160         73
JP163         72
JP164         79
JP165         73
JP166         72
JP168         75
JP169         73
JP170         72
JP171         80
JP172         76
JP173         73
JP174         73
JP175         73
JP176         73
JP177         74
JP178         73
KLB81         81
KLB82         72
JP113         73
JP114         73
JP115         73
JP116         73
JP117         73
JP118         74
JP120         73
JP179         74
JP180         73
JP182         73
JP184         73
JP185         73
JP186         73
JP188         73
JP190         73
JP192         73
JP194         73
JP196         73
JP198         73
JP200         73
JP248         73
JP249         73
JP250         73
JP251         74
JP252         73
JP253         73
JP254         73
JP29          73
JP30          73
JP31          73
JP32          73
JP34          73
JP35          73
JP37          74
JP38          74
JP39          73
JP40          73
JP41          73
JP42          73
JP43          73
JP44          73
JP45          79
JP46          73
JP48          73
JP49          73
JP50          83
JP51          73
JP52          74
JP53          73
JP54          74
JP55          73
JP56          73
JP57          79
JP58          73
JP59          73
JP60          69
KLB100        73
KLB101        73
KLB102        73
KLB103        73
KLB104        73
KLB105        82
KLB107        73
KLB109        73
KLB110        73
KLB111        73
KLB112        69
KLB113        73
KLB114        73
KLB115        73
KLB116        73
KLB117        73
KLB118        73
KLB119        73
KLB120        73
KLB121        73
KLB122        74
KLB123        74
KLB124        73
KLB125        73
KLB126        73
KLB127        73
KLB23         73
KLB24         73
KLB34         73
KLB39         77
JP121a        73
JP122a        73
JP123a        73
JP124a        79
JP125a        73
JP126a        82
JP127a        82
JP128a        77
JP129a        73
JP130a        76
JP131a        73
JP132a        80
JP133a        80
JP134a        80
JP135a        79
JP136a        83
JP137a        81
JP138a        76
JP139a        77
JP140a        76
JP141a        83
JP142a        76
JP143a        81
JP144a        84
JP145a        85
JP146a        76
JP147a        82
JP148a        84
JP149a        73
JP150a        85
JP151a        74
JP152a        85
JP153a        74
JP154a        84
JP155a        86
JP156a        86
JP157a        76
JP158a        84
JP159a        81
JP160a        85
JP163a        86
JP164a        79
JP165a        77
JP166a        77
JP168a        81
JP169a        73
JP170a        77
JP171a        84
JP172a        85
JP173a        73
JP174a        78
JP175a        80
JP176a        85
JP177a        76
JP178a        80
KLB81a        84
KLB82a        73
JP113a        80
JP114a        78
JP115a        75
JP116a        73
JP117a        76
JP118a        82
JP120a        73
JP179a        81
JP180a        82
JP182a        74
JP184a        73
JP185a        73
JP186a        74
JP188a        73
JP190a        74
JP192a        74
JP194a        79
JP196a        79
JP198a        73
JP200a        73
JP248a        76
JP249a        74
JP250a        79
JP251a        84
JP252a        73
JP253a        73
JP254a        73
JP29a         73
JP30a         73
JP31a         73
JP32a         73
JP34a         79
JP35a         85
JP37a         79
JP38a         74
JP39a         73
JP40a         73
JP41a         73
JP42a         85
JP43a         83
JP44a         79
JP45a         79
JP46a         74
JP48a         73
JP49a         82
JP50a         85
JP51a         83
JP52a         84
JP53a         84
JP54a         74
JP55a         82
JP56a         83
JP57a         79
JP58a         73
JP59a         74
JP60a         69
KLB100a       73
KLB101a       78
KLB102a       73
KLB103a       73
KLB104a       73
KLB105a       84
KLB107a       73
KLB109a       84
KLB110a       73
KLB111a       74
KLB112a       74
KLB113a       74
KLB114a       74
KLB115a       74
KLB116a       82
KLB117a       73
KLB118a       73
KLB119a       73
KLB120a       73
KLB121a       73
KLB122a       74
KLB123a       74
KLB124a       75
KLB125a       73
KLB126a       75
KLB127a       74
KLB23a        82
KLB24a        82
KLB34a        73
KLB39a        85

[Jessica da Silva]

HI Karen,

I'm not sure if this would be of great help, but have you checked that your individual data starts on line 11 for each line after the locus information line? The name of each sample should only take up 10 characters, including spaces. When I copied and pasted your information into notepad I noticed the information started much further along. I'm not sure if this is because you cut and pasted into an email.

Jessica

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Jessica da Silva
PhD Candidate

Molecular Ecology & Evolution Program
Applied Biodiversity Research
Kirstenbosch Research Centre

South African National Biodiversity Institute

Postal address: 

3 Sangster Road

Howick, KZN

3290

Home/Fax: +27 33 330 2230

Cell: +27 79 045 1781

Email: jessica....@gmail.com
          j.da...@sanbi.org.za

 

Website: http://jmdasilva.doodlekit.com/home/home

[shobhit]

hi karen and jess

i didnt really read through both your input files thoroughly but i have just one suggestion try using PGDspider or CONVERT to make your IMa2 files, there are sometimes spacing problems and hidden character problems in infiles created on different systems and texteditors.. the aforementioned programs help you to avoid most problems when creating infiles esp with names and the spaces between names and also converting fragment lenghts into repeat units...

link to pgdspider

http://www.cmpg.unibe.ch/software/PGDSpider/

additionally, its always better to code your fragment lengths in terms of repeat units.

cheers

s

[Jess]

Hi there,

Thanks for the suggestion of PGDSpider.  It helped me identify the problem with my locus information line. All is running smoothly now.

Jess

[Karen]

Hi,

Thanks for the suggestions.  The PGDSpider program did the trick, although I had to do a bit of editing afterwards (it had converted all the 0's in my microsat repeat values into N), but once I did this the IMa program accepted it.  I still don't know what the problem was with the original file, maybe it was the spacing.

Thanks,

Karen.