Dear all, I received requests for the answers to my STRUCTURE Batch run problem so below I have pasted 7 different solutions sent by different persons. Thanks to everyone (Anne Duputi�, Tomas Hrbek, Xianfa Xie, Alan Meerow, Alan Wilton, Robert H. Kraus, Alain Frantz, Elizabeth, J�rg Br�n, Pamela Wiener) for their attention to that problem. 1- I had the same problem, regardless of the version of Structure, but it disappeared when I put my working directory (the one with the datafile and where structure has to put its results) at the root of the computer (on the same disk as the one where Structure is installed). 2- I have encountered the same problem as you. It only occurs with version 2.2, version 2.1 is behaving normally. About three months ago I wrote to Pritchard about it, but never got a response. What I think is going on is that some of the Java routines are not getting initialized correctly by Structure, and so it does not execute properly. I have solved this by running another Java based program first. I usually run FigTree from Beaumont. Next time I open Structure it executes normally. I do not know if you have encountered this as well, but Structure 2.2 will not initialize from the shortcut, but has to be started directly from the .bat file. 3- I once experienced some similar problem. It seems that the program just did not get started successfully at the very beginning possibly due to some glitch in the program. I restarted the program and tried again, that usually solved the problem for me. 4- I also had the exact same problem on two different machines, and got in touch with Pritchard's programmer - he made a suggestion, which didn't seem to overcome the problem (check and see if an updated version has been posted - I haven't). His suggestion is sitting on my work computer - I am home and can't access those archived emails. I did a partial workaround by only specifying half of my desired k values in the batch - then the batch run went to completion. I then did did the second half, also without a problem. Don't know if there is some issue past a threshold value for the number of jobs in batch runs, but try my workaround and see if it succeeds on your machine. 5- I find there are some values of K for some runs it just won't run for. eg it will do a run with K values 1 to 7 and it works but not if I do K = 8 but will work for K=9 ? So just try dropping a few K values. 6- I also remeber having trouble with Structure like this. In my case I had a large dataset and a high k to run. When I tried that, the smaller k's ran without a problem, but the larger k's, fro a certain point just did nothing. The problem was allocated system memory. There is the structure.bat file in the main directory of strucutre. If you open that with an editor, it will say something like: jre\bin\java -Xmx256m -classpath class\structure.jar RunStructure This "Xmx256m" part was my problem last year. It says, it will allocate 256MB of RAM to the software, which was not enough for larger datasets. I changed it to "Xmx1024m" and it worked. It was structure 2.1. 7- I have had a similar problem of batch runs in STRUCTURE not starting. If you just close and re-open STRUCTURE, re-open the project and start another batch job, it should start the second time time round. Or at least it did when I tried it. In my case, with my original installation, solution 2 to 7 did not work. I then tried solution 1. I have three hard drives and Installing Structure on 2 of them (working directory and structure.exe on the same hard drive) did not work. Installing Structure on the third one worked but not all the time. I sometimes have to start again the program for the Batch run to work. Thanks again Sebastien. -- S�bastien Puechmaille UCD School of Biological and Environmental Sciences University College Dublin (Zoology) UCD Science and Education Research Center (West) Belfield Dublin 4 Ireland http://batlab.ucd.ie/~spuechmaille/ s.puechmaille@gmail.com