Error: gtf_to_fasta returned an error.

[hathiram2]

Hi Sphil,

I tried with the same names of index and GTF files, but still I get same error message. Can't understand anything that whys this happening

[hathiram2]

Thanks sphil,,

Yes,,they have different names..
Let em try with same names..

[sphil]

Did you check that the names of the index and the GTF file are the same? That is the most common problem. (And don't assume they are the same just because you downloaded the files from somewhere...)

[hathiram2]

Hello guys,

I am Hathi, a postdoc in EMBL, Heidelberg.

I am doing alignment of my RNA-Seq data from Arabidopsis with Tophat


I gave the following command

tophat -G genes.gtf -p 5 -o controlone genome
C2AFAACXX_Hr-02_13s004770-1-1_ram_lane313s004770_sequence.fastq,C2AFAACXX_Hr-02_13s004770-2-1_ram_lane513s004770_sequence.fastq

Genes.gtf is gene annotation file, while bowtie2 index files are starting with 'genome' name.

These both the files were downloaded from this link

http://tophat.cbcb.umd.edu/igenomes.shtml

and the out put looks like this

[2013-08-27 15:23:42] Beginning TopHat run (v2.0.9)
-----------------------------------------------
[2013-08-27 15:23:42] Checking for Bowtie
Bowtie version: 2.1.0.0
[2013-08-27 15:23:42] Checking for Samtools
Samtools version: 0.1.19.0
[2013-08-27 15:23:42] Checking for Bowtie index files (genome)..
[2013-08-27 15:23:42] Checking for reference FASTA file
[2013-08-27 15:23:42] Generating SAM header for genome
format: fastq
quality scale: phred33 (default)
[2013-08-27 15:23:42] Reading known junctions from GTF file
[2013-08-27 15:23:45] Preparing reads
left reads: min. length=52, max. length=52, 58033296 kept reads
(3282 discarded)
[2013-08-27 15:36:32] Building transcriptome data files..
[FAILED]
Error: gtf_to_fasta returned an error.




Can anyone please tell me that where is the problem??

Thank you so much and look forward to your posts eagerly....