I run my RNA seq data for alignment and assembly with the below mentioned options. The cufflinks run is repeatedly showing "Multihit not found". Is this a serious issue.

tophat -p 12 -G Genes.gtf -o tophat_RABM --max-multihits 2 Genome R1.fastq R2.fastq

cufflinks -p 8 -o cufflinks_RABT --max-bundle-frags 1000000000000 --multi-read-correct tophat_RABM_/accepted_hits.bam