Closed:cufflink and cuffmerge error

Question

[santosh.bicnehu]

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.....