Cuffmerge Error

I use the latest cufflinks2.1.1 to run the cuffmerge, but I encountered many errors like below, and the cuffmerge terminated itself. I use tophat2.06/bowtie1.0. What can be wrong?

Warning: couldn't find fasta record for '17|NT_113930.1'!
Warning: couldn't find fasta record for '17|NT_113943.1'!
Warning: couldn't find fasta record for '19|NT_113949.1'!
Warning: couldn't find fasta record for '1|NT_113878.1'!
Warning: couldn't find fasta record for '1|NT_167207.1'!
Warning: couldn't find fasta record for '4|NT_113885.1'!
Warning: couldn't find fasta record for '4|NT_113888.1'!
Warning: couldn't find fasta record for '7|NT_113901.1'!
Warning: couldn't find fasta record for '8|NT_113907.1'!
Warning: couldn't find fasta record for '8|NT_113909.1'!
Warning: couldn't find fasta record for '9|NT_113911.1'!
Warning: couldn't find fasta record for 'Un|NT_113889.1'!
Warning: couldn't find fasta record for 'Un|NT_113923.1'!
Warning: couldn't find fasta record for 'Un|NT_113961.1'!
Warning: couldn't find fasta record for 'Un|NT_167208.1'!
Warning: couldn't find fasta record for 'Un|NT_167209.1'!
Warning: couldn't find fasta record for 'Un|NT_167210.1'!
Warning: couldn't find fasta record for 'Un|NT_167213.1'!
Warning: couldn't find fasta record for 'Un|NT_167214.1'!
Warning: couldn't find fasta record for 'Un|NT_167216.1'!
Warning: couldn't find fasta record for 'Un|NT_167217.1'!
Warning: couldn't find fasta record for 'Un|NT_167218.1'!
Warning: couldn't find fasta record for 'Un|NT_167221.1'!
Warning: couldn't find fasta record for 'Un|NT_167222.1'!
Warning: couldn't find fasta record for 'Un|NT_167235.1'!
Warning: couldn't find fasta record for 'Un|NT_167236.1'!
Warning: couldn't find fasta record for 'Un|NT_167243.1'!

cuffmerge

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updated 12.8 years ago by Devon Ryan

• written 12.8 years ago by newDNASeqer

1 answer

Your reference annotation and reference sequence are from different places/not compatible.

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written 12.8 years ago by Devon Ryan

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