freebayes-parallel issue

[osekulovic]

Hello, snippy was working great - I then ran brew update and things went downhill. This is the error (and see log):

Running: freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 -F 0.05 --min-coverage 10 --min-repeat-entropy 1.0 -q 13 -m 60 --strict-vcf   -f reference/ref.fa snps.bam > snps.raw.vcf 2>> snps.log
[21:38:58] Error running command, check ./Cneg_ord_REF/A2/snps.log

I uninstalled snippy, freebayes and vcflib and run again brew install snippy and got freebayes and vcflib dependences.

snippy --check says Dependences look good! Running freebayes alone does not produce an error. Running snippy 4.6 on Linux.

Thanks in advance snps.log