problem with cuffmerge

Question

[zizigolu]

Sorry please help me to figure out this error,

I am running cuffmerge, for arabidopsis its ok but even by providing everything for yeast, permanently I get this error

[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$ cuffmerge -g genes.gtf -s genome.fa -p 8 assemblies.txt
[Tue Dec 22 16:25:02 2015] Beginning transcriptome assembly merge
-------------------------------------------

[Tue Dec 22 16:25:02 2015] Preparing output location ./merged_asm/
[Tue Dec 22 16:25:02 2015] Converting GTF files to SAM
[16:25:02] Loading reference annotation.
[Tue Dec 22 16:25:02 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_fileeOjgJA 
[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_fileeOjgJA doesn't appear to be a valid BAM file, trying SAM...
[16:25:03] Loading reference annotation.
[16:25:03] Inspecting reads and determining fragment length distribution.
Processed 6366 loci.                        
> Map Properties:
>    Normalized Map Mass: 4885.00
>    Raw Map Mass: 4885.00
>    Fragment Length Distribution: Truncated Gaussian (default)
>                  Default Mean: 200
>               Default Std Dev: 80
[16:25:03] Assembling transcripts and estimating abundances.
Processed 6366 loci.                        
[Tue Dec 22 16:25:07 2015] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
No fasta index found for genome.fa. Rebuilding, please wait..
Fasta index rebuilt.
Warning: couldn't find fasta record for 'Mito'!
[Tue Dec 22 16:25:08 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 'Mito'!
[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$

[Thibault D.]

Hi,

You have a sequence called 'Mito' in your file genes.gtf that is not present in your genome.fa, don't you ? (have a quick look with grep)

[zizigolu]

yes thank you,

[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$ awk -F "\t" '{print $1}' genes.gtf | uniq
I
II
III
IV
IX
Mito
V
VI
VII
VIII
X
XI
XII
XIII
XIV
XV
XVI
[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$ cat genome.fa | grep ">"
>I
>II
>III
>IV
>IX
>MT
>V
>VI
>VII
>VIII
>X
>XI
>XII
>XIII
>XIV
>XV
>XVI
[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$

I edited that I am running again, I hope it works...