Hi,

I downloaded gtf and genome.fa for yeast already but after trying many fastq files again I get the same error

May you tell me the reason please?

[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$ cuffmerge -g genes.gtf -s genome.fa -p 8 assemblies.txt
[Fri Dec  4 16:33:30 2015] Beginning transcriptome assembly merge
-------------------------------------------
[Fri Dec  4 16:33:30 2015] Preparing output location ./merged_asm/
[Fri Dec  4 16:33:32 2015] Converting GTF files to SAM
[16:33:32] Loading reference annotation.
[Fri Dec  4 16:33:32 2015] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o ./merged_asm/ -F 0.05 -g genes.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_fileQa29pl 
[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_fileQa29pl doesn't appear to be a valid BAM file, trying SAM...
[16:33:33] Loading reference annotation.
[16:33:35] Inspecting reads and determining fragment length distribution.
Processed 37276 loci.                       
> Map Properties:
>    Normalized Map Mass: 37330.00
>    Raw Map Mass: 37330.00
>    Fragment Length Distribution: Truncated Gaussian (default)
>                  Default Mean: 200
>               Default Std Dev: 80
[16:33:35] Assembling transcripts and estimating abundances.
Processed 37276 loci.                       
[Fri Dec  4 16:33:58 2015] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
Warning: couldn't find fasta record for 'I'!
Warning: couldn't find fasta record for 'II'!
Warning: couldn't find fasta record for 'III'!
Warning: couldn't find fasta record for 'IV'!
Warning: couldn't find fasta record for 'IX'!
Warning: couldn't find fasta record for 'MT'!
Warning: couldn't find fasta record for 'V'!
Warning: couldn't find fasta record for 'VI'!
Warning: couldn't find fasta record for 'VII'!
Warning: couldn't find fasta record for 'VIII'!
Warning: couldn't find fasta record for 'X'!
Warning: couldn't find fasta record for 'XI'!
Warning: couldn't find fasta record for 'XII'!
Warning: couldn't find fasta record for 'XIII'!
Warning: couldn't find fasta record for 'XIV'!
Warning: couldn't find fasta record for 'XV'!
Warning: couldn't find fasta record for 'XVI'!
[Fri Dec  4 16:34:07 2015] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
Warning: couldn't find fasta record for 'I'!
Warning: couldn't find fasta record for 'II'!
Warning: couldn't find fasta record for 'III'!
Warning: couldn't find fasta record for 'IV'!
Warning: couldn't find fasta record for 'IX'!
Warning: couldn't find fasta record for 'MT'!
Warning: couldn't find fasta record for 'V'!
Warning: couldn't find fasta record for 'VI'!
Warning: couldn't find fasta record for 'VII'!
Warning: couldn't find fasta record for 'VIII'!
Warning: couldn't find fasta record for 'X'!
Warning: couldn't find fasta record for 'XI'!
Warning: couldn't find fasta record for 'XII'!
Warning: couldn't find fasta record for 'XIII'!
Warning: couldn't find fasta record for 'XIV'!
Warning: couldn't find fasta record for 'XV'!
Warning: couldn't find fasta record for 'XVI'!