create-hybrid: option -G not recognized

[dhadsell]

I am trying to use EMASE on RNA-seq data obtained from F1 progeny of a cross between C57BL/6J and PL/J

First in g2gtools I used Mus_musculus.GRCm38.dna.primary_assembly.fa as the reference genome in vcf2vci and my variant file was generated from WGS data on PL/J (hq_common_PL_J.vcf.gz). I passed the output from this through patch, transform, and convert to create PL_J.transformed.fa and PL_J.gtf.

These were then used in EMASE create hybrid as follows:

#Define parameters
GENOME1=Mus_musculus.GRCm38.dna.primary_assembly.fa
GENOME2=PL_J.transformed.fa
GTF1=Mus_musculus.GRCm38.100.gtf
GTF2=PL_J.gtf
SUFFIX1=B6
SUFFIX2=PL
EMASE_DIR=B6PLF1

#loading anaconda for use in the job
module load anaconda

#activating emase
source activate emase

#Build pooled transriptome for B6PLF1
create-hybrid -G ${GENOME1},${GENOME2} -g ${GTF1},${GTF2} -s ${SUFFIX1},${SUFFIX2} -o ${EMASE_DIR}

#Leaving the emase environment
source deactivate

The command fails and returns "create-hybrid: option -G not recognized.

Can you please help me solve this issue?

[yumingcao]

They removed this option, you can run it successfully without -G. Yet I'm very confused why that is, and I found no explanations and updates from the developers.