Good day all! I'm running RSEM as a batch job on a cluster:

rsem-prepare-reference --gtf /home/tbeckett/lustre/honours_project/RSEM/ref/Mus_musculus.GRCm39.103.chr.gtf --bowtie2 --bowtie2-path software/bowtie2/2.3.4 \ /home/tbeckett/lustre/honours_project/RSEM/ref/Mus_musculus.GRCm39.dna.toplevel.fa /home/tbeckett/lustre/honours_project/RSEM/ref/mouse_ref

I recieved an error: Transcript ENSMUST00000132294 is out of chromosome 7's boundary!

Any idea what this error might be?

Also, the second line when specifying bowtie, software/bowtie2/2.3.4, what is the point of specifying 'software'? im copying it from a tutorial.

Help will be appreciated!