Question: cuffmerge error for loading annotation file
0
gravatar for nikhilvgbt
4.2 years ago by
nikhilvgbt0
India
nikhilvgbt0 wrote:

Hi,

I am trying to run cuffmerge but i am getting the error as follow.... could you please tell me the whats the problem and how can i solve this error ??

this is the command i used for cuffmerge;

cuffmerge -g hg19.gtf -s hg19.fa -p 8 assemblies.txt

and main error is;

[Mon Jan 26 22:40:49 2015] Beginning transcriptome assembly merge

-------------------------------------------

[Mon Jan 26 22:40:49 2015] Preparing output location ./merged_asm/
[Mon Jan 26 22:40:55 2015] Converting GTF files to SAM
[22:40:55] Loading reference annotation.
[22:40:56] Loading reference annotation.
[Mon Jan 26 22:40:58 2015] Quantitating transcripts
Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v2.2.1 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu).
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g hg19.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_fileMgq1Io 
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileMgq1Io doesn't appear to be a valid BAM file, trying SAM...
[22:40:59] Loading reference annotation.
    [FAILED]
Error: could not execute cufflinks
rna-seq samtools cufflinks • 2.9k views
ADD COMMENTlink modified 4.2 years ago by RamRS21k • written 4.2 years ago by nikhilvgbt0

Do you have the hg19.gtf file in the folder you're running cufflinks in?

ADD REPLYlink written 4.2 years ago by RamRS21k

@RamRS ... 

i have both the files .gtf and .fa files in working directory.... but when i run the command the error is shown.....

ADD REPLYlink written 4.2 years ago by nikhilvgbt0

Did you check the link from my other comment?

ADD REPLYlink written 4.2 years ago by RamRS21k

Also, take a look at this: http://seqanswers.com/forums/showthread.php?t=11694

ADD REPLYlink written 4.2 years ago by RamRS21k

hi RamRS; 

i checked that in forum and i tried accordingly but still same error... as far as i understood there is problem in the output of tophat which is .bam file or else output of the Cufflinks ...

ADD REPLYlink written 4.2 years ago by nikhilvgbt0

Could you also give us the exact command you used?

ADD REPLYlink written 4.2 years ago by RamRS21k

are you using .gtf and .fa from same source ?

ADD REPLYlink written 4.2 years ago by Manvendra Singh2.0k

Ah yeah the old problem.

ADD REPLYlink written 4.2 years ago by RamRS21k
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