Question: error in cuffmerge
0
gravatar for F
3.3 years ago by
F3.4k
Iran
F3.4k wrote:

hi,

i downloaded gtf and genome.fa for yeast already but after trying many fasqt file 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'!
[izadi@lbox161 cufflinks-2.2.1.Linux_x86_64]$ 

cuffmerge rna-seq • 1.4k views
ADD COMMENTlink written 3.3 years ago by F3.4k
1

probably a chromosome naming mess up. Check the chromosome names for your fasta file, against your input gtf. 

ADD REPLYlink written 3.3 years ago by andrew.j.skelton735.5k

thank you, but both containing the same chromosome names

ADD REPLYlink written 3.3 years ago by F3.4k
1

Including the GTF that you ran Cufflinks against?

ADD REPLYlink written 3.3 years ago by andrew.j.skelton735.5k

yes i checked 

ADD REPLYlink written 3.3 years ago by F3.4k
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