Calculating SFS using arlecore using example files

[Tony Einfeldt]

I am trying to run arlecore on Linux (Ubunto 16.10) to calculate SFS for observed values to be used in fastcoalsim2.

I am trying to calculate SFS on the example files from the Example_files_linux.zip package:
SFS/3PopDivNoMigr20Mb.arp
SFS/3PopDivNoMigr20Mb.ars

I copied these two files to the arlecore_linux folder, then ran the command:
./arlecore3522_64bit 3PopDivNoMigr20Mb.arp 3PopDivNoMigr20Mb.ars

A single message is displayed in terminal:
Arlecore terminated gracefully

The following files are produced:
arlequin.ini

arl_run.ars

arl_run.txt

3PopDivNoMigr20Mb.res/3PopDivNoMigr20Mb.js

3PopDivNoMigr20Mb.res/3PopDivNoMigr20Mb.xml

3PopDivNoMigr20Mb.res/3PopDivNoMigr20Mb_main.htm

3PopDivNoMigr20Mb.res/3PopDivNoMigr20Mb_tree.htm

3PopDivNoMigr20Mb.res/Arlequin_log.txt

The file 3PopDivNoMigr20Mb.res/Arlequin_log.txt reads:

Log file path: 3PopDivNoMigr20Mb.res/Arlequin_log.txt
Core Program Directory: /home/tony/arlecore_linux/
Random number generator initialized with lidum=-1125313
Reading project profile section...
done !
Opening next project...
3PopDivNoMigr20Mb.arp
////////////////////////////////////////////////////////////////////
RUN NUMBER 1 (21/09/17 at 14:17:37)
////////////////////////////////////////////////////////////////////


Reading Project: 
Reading input file ...
	Reading Samples section ...
	Reading Sample 1 ... 
	done ! (31 ms)

	Reading Sample 2 ... 
	done ! (22 ms)

	Reading Sample 3 ... 
	done ! (23 ms)

	done reading Samples section! (77 ms)
	Reading genetic structure ...
	done reading genetic structure! (0 ms)
done ! (77 ms)

------------------------------------------------------------------------
  Checking all selected options...
		Building vectors of alleles...
		done in 141 ms
  done!
  check selected settings...
  done!

Population 'Sample 1' : 
done in 0 ms

Population 'Sample 2' : 
done in 0 ms

Population 'Sample 3' : 
done in 0 ms

////////////////////////////////////////////////////////////////////
END OF RUN NUMBER 1 (21/09/17 at 14:17:38))
Total computing time for this run : 0h 0m 0s 354 ms
////////////////////////////////////////////////////////////////////

Successful run of 3PopDivNoMigr20Mb.arp

There do not appear to be any results. Does anyone know what I'm doing wrong?

Thanks,

Tony

[Miranda Sherlock]

Hi Tony - did you ever resolve this?

Miranda

[mirandabs]

Just fyi - I was using Arlecore on Mac & unix when I encountered the issue. I tried using Windows GUI of Arlequin and this resolved the issue.