PhyloCSF fails with GSL_exn exception

[iljungr]

Run PhyloCSF with parameters "100vertebrates" and the attached 2-codon fasta alignment.
chr19-44274475-44274480-.hg38_100.txt
It fails with this message:
exception 0 5 Error.Gsl_exn(_)
failure Failure("no regions successfully evaluated")
This occurs using the latest version of PhyloCSF as of 2017-01-12.
The alignment is the 100-vertebrates alignment of the 2 codons in hg38 chr19:44274475-44274480 on the - strand. If I run on either codon separately it works OK, but the two together give the exception. It also works OK with strategy=fixed (or omega). It also works if I exclude the final species (Lamprey).

I get the same exception when running on any of the following 21 regions of hg38 (using the 100vertebrates parameters):
chr19:44274142-44274207 - exception 0 65 Error.Gsl_exn()
chr19:44274475-44274654 - exception 0 179 Error.Gsl_exn()
chr5:140841378-140842178 - exception 0 800 Error.Gsl_exn()
chr5:140842216-140843655 + exception 0 1439 Error.Gsl_exn()
chr5:140848537-140850837 - exception 0 2300 Error.Gsl_exn()
chr5:141214369-141214965 - exception 0 596 Error.Gsl_exn()
chr5:141214979-141216433 + exception 0 1454 Error.Gsl_exn()
chr5:141214981-141216435 - exception 0 1454 Error.Gsl_exn()
chr8:143864557-143865003 - exception 0 446 Error.Gsl_exn()
chrM:5906-7438 - exception 0 1532 Error.Gsl_exn()
chrM:10061-10402 - exception 0 341 Error.Gsl_exn()
chrM:10832-10876 + exception 0 44 Error.Gsl_exn()
chr10:122631032-122631058 + exception 0 26 Error.Gsl_exn()
chr10:122631113-122631142 + exception 0 29 Error.Gsl_exn()
chr10:122630969-122631217 + exception 0 248 Error.Gsl_exn()
chr10:122630971-122631219 - exception 0 248 Error.Gsl_exn()
chr5:140842104-140842175 - exception 0 71 Error.Gsl_exn()
chr5:141215086-141215097 - exception 0 11 Error.Gsl_exn()
chr8:143864710-143864808 - exception 0 98 Error.Gsl_exn()
chr3:46811720-46811872 + exception 0 152 Error.Gsl_exn()
chr7:144299390-144300028 - exception 0 638 Error.Gsl_exn(_)