Thread: Cuffmerge error
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Old 03-31-2015, 09:29 AM   #1
cbaudo
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Location: Missouri

Join Date: Jan 2013
Posts: 21
Default Cuffmerge error

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?
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