BeagleStep error: "REF field is not a sequence of A, C, T, G, or N"

[brainfood]

This error appears to be separate from the original issue in which it was discussed. I moved it into its own issue.

I had been running CAMPAREE with only one sample. After reading your comment, I introduced another sample to see if the error would be solved. However, now I am getting a different error, also at the Beagle step.
BeagleStep.log
BeagleStep.serial.err.txt
BeagleStep.serial.out.txt

Originally posted by @Argonvi in #3 (comment)

[brainfood]

Looking in the BeagleStep.log file, it appears Beagle starts to process the variants (which is further than it got in the original issue), but fails when it encounters an entry in the variants file. Here's the pertinent entry from the log file:

ERROR: REF field is not a sequence of A, C, T, G, or N characters at chr2:233143703 [W]

It might be easiest to see if I can replicate this error on my end. Are the data you're using to run CAMPAREE publicly available? If so, would you please direct me toward the data? I would also need the specific version of CAMPAREE you're running, a copy of the config file you're using to run CAMPAREE, and the command you used to launch CAMPAREE. If you have any concerns about posting these data in a public forum, let me know and we can work out an alternative.

[Argonvi]

The data are not publicly available but I can sare them with you privately, if that is ok with you.