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Old 11-16-2013, 09:24 AM   #1
Location: Ann Arbor

Join Date: Oct 2013
Posts: 21
Default run cuffmerge gives such error message

[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>
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?
liweixie is offline   Reply With Quote
Old 11-17-2013, 10:35 PM   #2
Location: Germany

Join Date: Jan 2013
Posts: 42

Could you please also post the command you used?
sBeier is offline   Reply With Quote
Old 07-24-2014, 07:45 AM   #3
Location: Boston

Join Date: Jan 2014
Posts: 13

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";'

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

Anybody know how to resolve it?

BADE is offline   Reply With Quote
Old 07-24-2014, 05:08 PM   #4
Location: Guangzhou China

Join Date: Aug 2013
Posts: 82

What's in your assemblies.txt file??

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