Question: cufflink and cuffmerge error
0
gravatar for santosh.bicnehu
2.9 years ago by
santosh.bicnehu0 wrote:

Hi everyone,

I am getting an error while running cuffmerge with the follwing options:

cuffmerge -g genes.gtf -s genome.fa -p 2 assembled_tc.txt

this is the output in the terminal after execution with error

[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_filehLSwCc doesn't appear to be a valid BAM file, trying SAM...

[Fri Jun 10 20:37:35 2016] Beginning transcriptome assembly merge

-------------------------------------------

[Fri Jun 10 20:37:35 2016] Preparing output location ./merged_asm/

[Fri Jun 10 20:37:38 2016] Converting GTF files to SAM

[20:37:38] Loading reference annotation.

[20:37:38] Loading reference annotation.

[20:37:38] Loading reference annotation.

[20:37:38] Loading reference annotation.

[Fri Jun 10 20:37:39 2016] 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 2 ./merged_asm/tmp/mergeSam_filehLSwCc 

[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_filehLSwCc doesn't appear to be a valid BAM file, trying SAM...

[20:37:39] Loading reference annotation.

[20:37:48] Inspecting reads and determining fragment length distribution.

Processed 31327 loci.                       

Map Properties:
Normalized Map Mass: 17178.00

Raw Map Mass: 17178.00

Fragment Length Distribution: Truncated Gaussian (default)

Default Mean: 200

Default Std Dev: 80

[20:37:48] Assembling transcripts and estimating abundances.

Processed 31327 loci.  

[Fri Jun 10 20:39:16 2016] 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.
[Fri Jun 10 20:39:35 2016] Comparing against reference file genes.gtf
You are using Cufflinks v2.2.1, which is the most recent release.

plz help me to troubleshoot the same.....

rna-seq cuffmerge cufflink • 1.2k views
ADD COMMENTlink modified 2.6 years ago by stefanysolano.cr0 • written 2.9 years ago by santosh.bicnehu0

Can you describe the contents of assembled_tc.txt file? These are the locations of transcripts.gtf files from Cufflinks, right? Can you also confirm that the gtf files and fasta files that you used were from the same genome build?

ADD REPLYlink written 2.6 years ago by Satyajeet Khare1.3k
0
gravatar for stefanysolano.cr
2.6 years ago by
stefanysolano.cr0 wrote:

I have exactly the same problem! Has someone found any way to fix it?

ADD COMMENTlink written 2.6 years ago by stefanysolano.cr0
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