Thread: cuffmerge error
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Old 06-05-2013, 08:06 PM   #1
Baoqing
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Location: Texas

Join Date: Jan 2013
Posts: 24
Default cuffmerge error

Hi, All

I was trying to run the cuffmerge for my two samples. However, there is warning message point to the mitochondrial genome, however, i could not figure out the exact problem, could you please give some hints? I directly download the Saccharomyces cerevisiae/Ensembl/EF4, ref genome.

Thank you very much!

bq@bq-VirtualBox:~/Desktop/rnaseq/trimmed$ cuffmerge -g genes.gtf -s genome.fa -p 4 assemblies.txt

[Wed Jun 5 22:46:37 2013] Beginning transcriptome assembly merge
-------------------------------------------

[Wed Jun 5 22:46:37 2013] Preparing output location ./merged_asm/
[Wed Jun 5 22:46:37 2013] Converting GTF files to SAM
[22:46:37] Loading reference annotation.
[22:46:37] Loading reference annotation.
[Wed Jun 5 22:46:37 2013] Quantitating transcripts
You are using Cufflinks v2.1.1, 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 4 ./merged_asm/tmp/mergeSam_fileDalcVi
[bam_header_read] EOF marker is absent.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
File ./merged_asm/tmp/mergeSam_fileDalcVi doesn't appear to be a valid BAM file, trying SAM...
[22:46:37] Loading reference annotation.
[22:46:38] Inspecting reads and determining fragment length distribution.
Processed 2290 loci.
> Map Properties:
> Normalized Map Mass: 6966.00
> Raw Map Mass: 6966.00
> Fragment Length Distribution: Truncated Gaussian (default)
> Default Mean: 200
> Default Std Dev: 80
[22:46:38] Assembling transcripts and estimating abundances.
Processed 2290 loci.
[Wed Jun 5 22:46:43 2013] Comparing against reference file genes.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
Warning: couldn't find fasta record for 'Mito'!
[Wed Jun 5 22:46:44 2013] Comparing against reference file genes.gtf
You are using Cufflinks v2.1.1, which is the most recent release.
Warning: couldn't find fasta record for 'Mito'!
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