run cuffmerge gives such error message

[liweixie]

[Sat Nov 16 13:22:30 2013] Beginning transcriptome assembly merge
-------------------------------------------

[Sat Nov 16 13:22:30 2013] Preparing output location ./merged_asm/
Traceback (most recent call last):
File "/Users/liweixie/documents/bioinformatics/folder/cufflinks-2.1.1/cuffmerge", line 580, in <module>
sys.exit(main())
File "/Users/liweixie/documents/bioinformatics/folder/cufflinks-2.1.1/cuffmerge", line 538, in main
gtf_input_files = test_input_files(transfrag_list_file)
File "/Users/liweixie/documents/bioinformatics/folder/cufflinks-2.1.1/cuffmerge", line 268, in test_input_files
g = open(line,"r")
IOError: [Errno 2] No such file or directory: 'chr1\tCufflinks\ttranscript\t29554\t31097\t1\t+\t.\tgene_id "ENSG00000243485.1"; transcript_id "ENST00000473358.1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";'
Any one knows what is going on with this?

[sBeier]

Could you please also post the command you used?

[BADE]

Same here:

IOError: [Errno 2] No such file or directory: '1\tCufflinks\ttranscript\t9896\t10296\t1000\t-\t.\tgene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "2.8891757020"; frac "1.000000"; conf_lo "1.286549"; conf_hi "4.491802"; cov "3.119611";'


Command:
cuffmerge -g genome.gtf -s genome.fa assemblies.txt

Anybody know how to resolve it?

BADE

[yueluo]

What's in your assemblies.txt file??

It appears that cuffmerge is reading a GTF when it expects the list of bamfiles.