I am just using a test input file when running my code, and everything seems to work okay except that when i make my input files very small freebayes takes a long time to run and misses mutations. So in my test file I just have a single read that aligns properly with samtools yielding this:

HISEQ:331:C85AMANXX:8:1101:2127:2132 0 chr4 110541172 60 120M * 0 0 AAACTCTTCATGCCAGTTCCCTGTCTCATCAGATAGATACTGAGGCCTCTAGGCATCAGCCGGATATCCCTAAGGACAGTGTTGGAGGAACTGCTGAGTGGATTCATGGTCAACTACCAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF<ffbfffffffffbfffff<fffffffffff nm:i:1="" md:z:38t81="" as:i:115="" xs:i:20<="" p="">

Then when I call freebayes in the following way, it will take ~15min to call variants, and will miss the two variants that I specifically put into the read.

system("%s -X -F 0.0000001 --fasta-reference %s %s > %s" % (freebayes, REF, bamOut, vcfOut))

With larger files everything seems to work okay, so I'm wondering if there is something I am missing with creating a small test file.