Question about using genome annotation for STAR mapping

[Gen B]

Hello,

I have some questions about using a genome annotation file (.gtf) as input for STAR genomeGenerate. I have a rhemac10 liftover annotation file that I got from another lab that I would like to combine with the NCBI rhemac10 genome annotation file to use when I map paired-end reads using STAR. I used the following command to concatenate both files into one gtf file. 

cat rheMac10.ncbiRefSeq.gtf rhemac10_liftover_annot.gtf >> combined_rhemac10_liftover_ncbi.gtf

I'm then using STAR to read in genomic (rheMac10.fa) and transcriptomic sequences (combined_rhemac10_liftover_ncbi.gtf) before alignment.

STAR --runMode genomeGenerate --genomeDir ./mapping/star_combined_gtf --genomeFastaFiles mapping/rhemac10/rheMac10.fa --sjdbGTFfile quants/combined_rhemac10_liftover_ncbi.gtf

When I run the STAR command, I keep getting errors like below.

# ./map_combined.sh: line 49: 250954 Killed                  STAR --runMode genomeGenerate --genomeDir ./mapping/star_combined_gtf --genomeFastaFiles mapping/rhemac10/rheMac10.fa --sjdbGTFfile quants/combined_rhemac10_liftover_ncbi.gtf
# 20 minutes and 53 seconds elapsed.

Is there something I'm doing wrong here? Do I need to sort the combined gtf file in chromosomal order before running the STAR command? Have you combined gtf files before for RNAseq data, and if so how would you recommend I do this?

Best,

Genevieve