After running cufflink for two samples of RNA-Seq data, I used cuffmerge and executed the following command

    cuffmerge -p 8 -g <directory>/<gff file>   -s <directory>/<refernec fasta file>  <directory>/assemblies.txt

Where `assemblies.txt` contains the `transcripts.gtf`

But I am getting following error

```
[Sun Jul 13 14:44:46 2014] Beginning transcriptome assembly merge
-------------------------------------------

[Sun Jul 13 14:44:46 2014] Preparing output location ./merged_asm/
[Sun Jul 13 14:46:04 2014] Converting GTF files to SAM
[14:46:04] Loading reference annotation.
[14:47:10] Loading reference annotation.
[14:48:06] Loading reference annotation.
[14:49:23] Loading reference annotation.
[14:50:29] Loading reference annotation.
[14:51:44] Loading reference annotation.
[Sun Jul 13 14:52:46 2014] 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 <directory>/<gff file> -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_file3DKFYb 
[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_file3DKFYb doesn't appear to be a valid BAM file, trying SAM...
[14:52:49] Loading reference annotation.
Error parsing strand (?) from GFF line:
IWGSC_CSS_1DS_scaff_731014      .       repeat_region   1       174     .       ?    .Name=trf;class=trf;repeat_consensus=ATTGGTATAGAACGCATGAAGAAACTCCATACAGATGGATCTTTAGACTCACTCAATTATGAAAAAATTGAGACATGCAAACCATGTCT;type=Tandem repeats
        [FAILED]
Error: could not execute cufflinks
```
You are using the wrong input file. You downloaded the GFF3 instead of GTF file. The correct file is: ftp://ftp.ensemblgenomes.org/pub/plants/release-22/gtf/triticum_aestivum/Triticum_aestivum.IWGSP1.22.gtf.gz

This is your GFF3 file:

```
##gff-version 3
IWGSC_CSS_5BS_scaff_1034127    .    repeat_region    61    200    .    +    .    Name=gnl|TREP|TREP3026;class=Unknown;repeat_consensus=N;type=Unknown
IWGSC_CSS_3AL_scaff_747250    .    repeat_region    2    200    .    +    .    Name=gnl|TREP|TREP765;class=Unknown;repeat_consensus=N;type=Unknown
IWGSC_CSS_3B_scaff_7107049    .    repeat_region    1    200    .    +    .    Name=gnl|TREP|TREP232;class=Unknown;repeat_consensus=N;type=Unknown
```

This is the GTF file:

```
IWGSC_CSS_6DL_scaff_127793    protein_coding    exon    526    645    .    +    .     gene_id "Traes_6DL_7FFFE462C"; transcript_id "Traes_6DL_7FFFE462C.2"; exon_number "1"; seqedit "false";
IWGSC_CSS_6DL_scaff_127793    protein_coding    CDS    574    645    .    +    0     gene_id "Traes_6DL_7FFFE462C"; transcript_id "Traes_6DL_7FFFE462C.2"; exon_number "1"; protein_id "Traes_6DL_7FFFE462C.2";
```