MFA alignment error

[gkkilaru]

Hello,

I wanted to use PhyloCSF on one of our cufflinks output data annotated with GENCODE.

The cufflinks output file was a *.GTF file and I converted it into *.fa using the gffread utility from cufflinks package.

Using the following command - ./PhyloCSF /path/PhyloCSF_Parameters/29mammals /path/cufflinksoutput.fa.

I am getting this error.

Failure("invalid MFA alignment: empty species name or sequence, or sequence length mismatch")

Any timely support is well appreciated.

Thanks
~Gokhul