Question
Asked 23rd Mar, 2015

Can anyone help with input file format for Msats & mtDNA in DIYABC?

Hi  everyone,
I've been working with Msats in DIYABC no problem but would like to try incorporating mtDNA sequences too, however I cannot seem to get the input file right. I've been following the instructions in the manual but get an error message every time I try to upload my file. Can anyone help? Many thanks! 

Most recent answer

10th Aug, 2020
Carolina Machado
Universidade Federal de São Carlos
Dear Sheila,
Unfortunately I had never see this issue. Did you try to write for DIYABC team?

All Answers (22)

27th Mar, 2015
Peter Shum
Liverpool John Moores University
Hi Hazel,
If you want to merge Microsatellites and mtDNA sequences you need to format the .txt file in the following way. 
Using a text editor like Programmers notepad 2 (http://www.pnotepad.org/download/) you can easily format the DIYABC input this way;
Name
Micro1 <A>
Micro2 <A>
SEQ  <M>
POP
sample ###### ###### <[GATC]>
sample ###### ###### <[GATC]>
POP
sample ###### ###### <[GATC]>
sample ###### ###### <[GATC]>
The brief above example shows a merged dataset of 3 loci, 2 microsatelite loci and 1 DNA sequence. Separated by their populations (POP) with their corresponding samples. Each sample name is separated (used tab key not space bar) by the data then followed by the allele genotypes and the sequence. (SEE ATTACHED EXAMPLE)
Hope this helps.
Peter
27th Mar, 2015
Hazel A Jackson
University of Kent
Hi Peter
Huge thanks! This is really helpful indeed. I realise I was using a genepop file exported from GenAlEx which was converting my genotypes into a four digit format, rather than the six digits specified for DIYABC. phew!
I am now encountering further problems.  Once my input file is uploaded, scenarios set, summary statistics selected etc..the program then won't run the computations.  It stays at 0%.  I am using the beta 2.04 version so am wondering if there is a bug.  I have tried on a MAC and PC and no luck which is very frustrating... have you had this experience, or do you use an earlier version of DIYABC?  
Once again, many thanks!
Hazel
27th Mar, 2015
Peter Shum
Liverpool John Moores University
Yes I think you still have a formatting issue. Try make sure your format adheres exactly to the example file I uploaded because if there are any special characters like (") in the dataset EXCLUDING the title line, that may be the cause which I have experienced before. I use the 2.04 version too.
P
30th Mar, 2015
Hazel A Jackson
University of Kent
 Hi Peter
I'm stumped! I still can't get the software to run.  I've tried with just msats or just tDNA and it just sits at 0%.  Weirdly I tried running it using an exported genepop 4 digit msat format from GenAlex, and it ran!?!? (but no if I include the mtDNA sequence data).
Could I send you a copy of my input file for your expert eye?..i'm getting desperate! I would be very grateful.  Hopefully its something stupidly obvious.
Thanks Peter, much appreciated.
Hazel
30th Mar, 2015
Peter Shum
Liverpool John Moores University
 Yes you can send me the data and I will have a look for you.
1st Apr, 2015
Hazel A Jackson
University of Kent
Hi Peter, just wanted to confirm I emailed you and that you received it (not nagging I promise!) thank you!
29th May, 2015
Carolina Machado
Universidade Federal de São Carlos
HI Hazel! Did you figure out this problem? I have the same it in my analysis. I try to generate the simulations and the progress bar keeps telling me 'Running ...'
and just stays there. It seems frozen.  =/
1st Jun, 2015
Hazel A Jackson
University of Kent
Hi Carolina, Yes indeed! Peter was a HUGE help and sorted out my input file for me.
Its very frustrating eh! If you pop me an email I am happy to send you one of my example input files for you to play with.  My email is hj61@kent.ac.uk
27th Nov, 2015
Carlos Eduardo Almeida
University of Campinas
 Hi all, 
I have had a hard time with DIYABC too. Indeed, I am not sure whether it is the most appropriated software for my goal: undertanding the diverstification process in a close related triatomine species complex. I just sent an email to Peter.
The best,
CEA
14th Mar, 2016
Ariel Ceferino Toloza
National Scientific and Technical Research Council
Hi all,
I´m having the same troubles as Hazel and Carolina. I got stuck during the running stage!. I sent a private mesage into the Diyabc web profile but haven´t received any answer, yet.
Could you please help me how to run my data?.
23rd Aug, 2016
Leonardo Machado
 Dears Ariel, Hazel and Carolina,
Did you  solve your problem in running DIYABC? My analysis is also frozen in the running stage. Can you tell me how you fix this?
Many thanks,
1 Recommendation
23rd Aug, 2016
Ariel Ceferino Toloza
National Scientific and Technical Research Council
Hi Leonardo,
I´m still stuck with the DIYABC analysis.....HELPPPPPPPP
5th Sep, 2016
Hazel A Jackson
University of Kent
Ariel - I'm so sorry, I've only just seen this.  Did you fix your problem?? 
9th Sep, 2016
Ariel Ceferino Toloza
National Scientific and Technical Research Council
Not yet..
13th Sep, 2016
Hazel A Jackson
University of Kent
pop me an email at hj203@kent.ac.uk
Happy to try and help if I can :-)
10th Oct, 2019
Ginushika Premarathne
Saga University
Anyone solved Diyabc problems.? please if have any information share with me. I am stuck with data file formats.
10th Oct, 2019
Carolina Machado
Universidade Federal de São Carlos
Hi Ginushika!
I have example files. If you need it, please, sent a email at carolbioms@gmail.com
2 Recommendations
11th Oct, 2019
Ginushika Premarathne
Saga University
Thank you Carolina.
26th Nov, 2019
Julia Tovar Verba
Ludwig-Maximilians-University of Munich
Carolina Machado , do you have example files for SNPs? Thanks!
26th Nov, 2019
Carolina Machado
Universidade Federal de São Carlos
Yes, I have. Send me a e-mail!
21st Jul, 2020
Sheila Rodríguez-Machado
Instituto de Ciencias del Mar
Hello everyone,
Carolina Machado , Hazel A Jackson , hope you can help me. I'm running DIYACB with mtDNA sequences and when I run the analysis to check for biases and precision, I got an error (see pic) at 28%. do you know what could be the problem?
Thanks in advance,
sheila

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