Cuffmerge Error

[rmart]

I am in the process of analysis my first RNA-seq experiment and have ran into an error with Cuffmerge that I just can't solve. I've read the threads of people who have had the same error and it hasn't seemed to help. So far I've aligned my reads using STAR-2.5.2b and used these to run Cufflinks with the command,

~/jgg-093-aa/cufflinks-2.2.1.Linux_x86_64/cufflinks \
	--library-type fr-firststrand -p 8 -G ~/jgg-093-aa/star/genome/genes.gtf \
	-o ~/jgg-093-aa/Cufflinks/Treatment1/ \
	~/jgg-093-aa/Aligned_Rn6/Treatment1Aligned.sortedByCoord.out.bam

This created a folder with the transcripts.gtf file for all of my samples. I am now trying to merge all these GTF files with Cuffmerge before going on to use Cuffdiff.

My Cuffmerge script that I have been trying to submit is:

~/jgg-093-aa/cufflinks-2.2.1.Linux_x86_64/cuffmerge \
	-g ~/jgg-093-aa/star/genome/genes.gtf -o ~/jgg-093-aa/Cufflinks/Master/  -s ~/jgg-093-aa/star/genome/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa \
	~/jgg-093-aa/Cufflinks/Assemblies.txt

Every time I try running this though, I get the following output:

[Thu Mar 23 17:05:51 2017] Beginning transcriptome assembly merge
-------------------------------------------

[Thu Mar 23 17:05:51 2017] Preparing output location /home/rmarti68/jgg-093-aa/Cufflinks/Master//
Traceback (most recent call last):
  File "/home/rmarti68/jgg-093-aa/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 580, in <module>
    sys.exit(main())
  File "/home/rmarti68/jgg-093-aa/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 538, in main
    gtf_input_files = test_input_files(transfrag_list_file)
  File "/home/rmarti68/jgg-093-aa/cufflinks-2.2.1.Linux_x86_64/cuffmerge", line 268, in test_input_files
    g = open(line,"r")
IOError: [Errno 2] No such file or directory: '~/jgg-093-aa/Cufflinks/Treatment1/transcripts.gtf'

I've doubled checked that the path to the transcripts.gtf file is correct and using the paths for the other components with Cufflinks and STAR worked.

Any help or advice is very appreciated.

Thanks!