Cuffmerge error

[cbaudo]

Hello, I am getting the following error message when using Cuffmerge:

cas-mw134-9sb9s:cufflinks-2.2.1.OSX_x86_64 bioadmin$ ./cuffmerge —p 30 -g genes_sort.gtf -s reference.txt assembly.txt

[Tue Mar 31 12:17:12 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Mar 31 12:17:12 2015] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "./cuffmerge", line 580, in <module>
sys.exit(main())
File "./cuffmerge", line 530, in main
transfrag_list_file = open(args[0], "r")
IOError: [Errno 2] No such file or directory: '\xe2\x80\x94p'

The assembly.txt file contains path information for the cufflinks output:
/Users/bioadmin/Desktop/cufflinks_results/2R4/transcripts.gtf
/Users/bioadmin/Desktop/cufflinks_results/2R5/transcripts.gtf
/Users/bioadmin/Desktop/cufflinks_results/2R6/transcripts.gtf
etc.

The log out file simply contains the command I entered into terminal. I'm using a system with 40GB of memory and 8 CPUs. Could you please help me identify the issue?

[sshankr]

Hello cbaudo,

I am facing a similar issue with Cuffmerge. The runs terminate within a sec and the run.log file only contains the command which I executed.

Were you able to resolve this issue?

[sshankr]

I was able to rectify this by specifying the -o option at the beginning, after cuffmerge.

[alexGrenoble]

is there a specific reason that different genes merge together in cuffmerge? Just because they are close to each other?

What I have is 3 different genes, that have the same assembled merged gene ID but have different transcripts.

I was expecting that since cuffmerge merges the gene IDs, it would merge the transcripts as well, and this could have been the reason that it merges the genes together. But in my case I get different assembled merged transcript IDs.

Any idea why?