MrBayes Restart REST interface:
This interface is used to restart a failed or "timed-out" MrBayes run. The interface requires the user to re-submit all of their existing MrBayes run files from the timed out job. We are working on a better way to manage this currently. To use the restart capability, please use the following steps exactly:
- Download the results from a MrBayes job that you wish to restart. Confirm that the results include a checkpoint (.ckp) file (it is possible for a job to terminate so early this file is not created, and it is also possible to turn checkpointing off via the MrBayes block. Please see the MrBayes manual for more details).
- Identify the files that will be required for a restart run. These are .ckp, .mcmc, and infile.nex and any files with the format .run.t, or .run.p, where is either infile.nex (default) or any string specified by the command filename= in your Nexus block.
- These files must be specified using the input file elements given below. For example, select .run1.t for the parameter upload_sumtfile1_ , and so forth. The names will be changed by the application to the format infile.nex.run1.t, infile.nex.run2.t and so forth.
- Before submitting, you must modify the infile.nex input file in two ways. First, in the mcmc command set in the MrBayes block, add the statement append=yes. Next, remove any filenames= commands in the MrBayes block.
- Once the run begins, you will see that two files will appear for each file you uploaded. For example, there will be an infile.nex.mcmc and an infile.nex.mcmc~ file. The file with the tilde (~) after it is a file created as part of the new run. The file without the tilde will be the file you uploaded, with the restart information appended to it. We apologize for this very cumbersome process, but we wanted to expose this capability as soon as possible.
The Tool ID for this interface is MRBAYES_321RESTARTBETA. It is selected with toolId=MRBAYES_321RESTARTBETA
Supported uploaded files:
infile_ - Primary Input File, this is the infile.nex, modified as described above.
upload_ckpfile_ - InFile - This is the Checkpoint File from the run to be restarted (.ckp)
upload_mcmcfile_ - InFile - This is the mcmc File from the run to be restarted (.mcmc)
upload_ssfile_ - InFIle - Choose the stepping stone file (.ss) (optional).
upload_sumpfile1_ - InFile - This is the first Sump File (.p), this file is required.
upload_sumpfile2_ - InFile - This is the second Sump File (.p), required if more than one is specifed.
upload_sumpfile3_ - InFile - This is the third Sump File (.p) required if more than two are specifed.
upload_sumpfile4_ - InFile - This is the fourth Sump File (.p) required if more than three are specifed.
upload_sumpfile5_ - InFile - This is the fifth Sump File (.p), required if more than four are specified.
upload_sumpfile6_ - InFile - This is the sixth Sump File (.p), required if more than five are specified.
upload_sumpfile7_ - InFile - This is the seventh Sump File (.p), required if more than six are specified.
upload_sumpfile8_ - InFile - This is the eigth Sump File (.p), required if more than seven are specified.
upload_sumpfile9_ - InFile - This is the ninth Sump File (.p), required if more than eight are specified.
upload_sumpfile10_ - InFile - This is the tenth Sump File (.p), required if more than nine are specified.
upload_sumpfile11_ - InFile - This is the eleventh Sump File (.p) required if more than ten are specified.
upload_sumpfile12_ - InFile - This is the twelfth Sump File (.p) required if more than eleven are specified.
upload_sumpfile13_ - InFile - This is the thirteenth Sump File (.p), required if more than twelve are specified.
upload_sumpfile14_ - InFile - This is the fourteenth Sump File (.p), required if more than thirteen are specified.
upload_sumpfile15_ - InFile - This is the fifteenth Sump File (.p), required if more than fourteen are specified.
upload_sumpfile16_ - InFile - This is the sixteenth Sump File (.p), required if more than fifteen are specified.
upload_sumpfile17_ - InFile - This is the seventeenth Sump File (.p), required if more than sixteen are specified.
upload_sumpfile18_ - InFile - This is the eighteenth Sump File (.p), required if more than seventeen are specified.
upload_sumpfile19_ - InFile - This is the nineteenth Sump File (.p) required if more than eighteen are specified.
upload_sumpfile20_ - InFile - This is the twentieth Sump File (.p) required if twenty are specified.
upload_sumtfile1_ - InFile - This is the first Sumt File (.t), this file is required.
upload_sumtfile2_ - InFile - This is the second Sumt File (.t), required if more than one is specifed.
upload_sumtfile3_ - InFile - This is the third Sumt File (.t) required if more than two are specifed.
upload_sumtfile4_ - InFile - This is the fourth Sumt File (.t) required if more than three are specifed.
upload_sumtfile5_ - InFile - This is the fifth Sumt File (.t), required if more than four are specified.
upload_sumtfile6_ - InFile - This is the sixth Sumt File (.t), required if more than five are specified.
upload_sumtfile7_ - InFile - This is the seventh Sumt File 3 (.t), required if more than six are specified.
upload_sumtfile8_ - InFile - This is the eigth Sumt File (.t), required if more than seven are specified.
upload_sumtfile9_ - InFile - This is the ninth Sumt File (.t), required if more than eight are specified.
upload_sumtfile10_ - InFile - This is the tenth Sumt File (.t), required if more than nine are specified.
upload_sumtfile11_ - InFile - This is the eleventh Sumt File (.t) required if more than ten are specified.
upload_sumtfile12_ - InFile - This is the twelfth Sumt File (.t) required if more than eleven are specified.
upload_sumtfile13_ - InFile - This is the thirteenth Sumt File (.t), required if more than twelve are specified.
upload_sumtfile14_ - InFile - This is the fourteenth Sumt File (.t), required if more than thirteen are specified.
upload_sumtfile15_ - InFile - This is the fifteenth Sumt File (.t), required if more than fourteen are specified.
upload_sumtfile16_ - InFile - This is the sixteenth Sumt File (.t), required if more than fifteen are specified.
upload_sumtfile17_ - InFile - This is the seventeenth Sumt File (.t), required if more than sixteen are specified.
upload_sumtfile18_ - InFile - This is the eighteenth Sumt File (.t), required if more than seventeen are specified.
upload_sumtfile19_ - InFile - This is the nineteenth Sumt File (.t) required if more than eighteen are specified.
upload_sumtfile20_ - InFile - This is the twentieth Sumt File (.t) required if twenty are specified.
Supported parameters are:
run_version_ - Excl - This specifes the verion of MrBayes, where MB=3.2.n, most recent verison is default, allowed values today are 6 or 3;
nruns_specified_ - Integer - My MrBayes Block specifies nruns= default=2
nchains_specified_ - Integer - My MrBayes Block specifies nchains= default=4, the product nruns*nchains must an be even number.
runtime_ - Float - Maximum Hours to Run (click here for help setting this correctly)
num_tfiles_ - Excl - How many Sumt files do you wish to upload? (1-20 is allowed, 1 is default).
num_pfiles_ - Excl - How many Sump files do you wish to upload? (1-20 is allowed, 1 is default).
