I am running BEAGLE 4.1 on data set with three groups. I ran a .vcf that has all three groups' data combined, which went without a hitch and I have great useable data. However, I also split up the main .vcf into three .vcfs for each group using R, to impute them individually. This is where I encountered my "error" - while one group (the largest) went normally, the imputation on the second group always stops early. The command prompt, when I check it, has the same line repeated as far up as I can scroll, which reads:
at dag.MergeableDag.similar<mergeabledag.java:374>
The run log does not have this line in it, nor does it list any error; rather, it just lists windows and iterations up to the last one it ran with no sign of why it cut off. BEAGLE does generate an output .vcf, which is truncated somewhere early on. Every time I run BEAGLE, the exact spot it ends on differs, though the output file is always truncated with the same repeated line in the terminal. Often (but not always), the last line in the imputed .vcf is the last SNP in a chromosome. I have looked at these lines in the input .vcf and noticed nothing special about them compared to others (no missing data or strange formatting).
I have so far tried restarting the computer several times, closing all processes, updating Java, and deleting/re-downloading the Beagle .jar, but the error persists. I am running Windows 7 Professional.
Has anyone had a similar error? What does it mean?
Thank you in advance!
Edit: It was pointed out in an email from Dr. Browning that this was likely a stack overflow error. I had not initially been using the -Xss option, but I added -Xss5m to my command prompt at his suggestion and the run worked.
This is the one place where adding an answer to your own question would be used :-)
I'll move your answer to an actual answer-post.