Question: Cuffmerge: invalid BAM binary header
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4.0 years ago by
biolab1.1k
biolab1.1k wrote:

Hi, everyone,

I ran cuffmerge with the command cuffmerge -g /data/TAIR10_GFF3_genes_transposons.gff -s /data/TAIR10.fa -p 8 assemblies.txt, However, I saw two error messages, which have been highlighted below.  I checked the headers of four BAM files (two replicates of wt and mutant), all of which are the same except the command line. I seek your help to inform me where is the wrong point.  Any suggestions and comments will be much appreciated.  Thanks.

[Tue Sep  1 10:53:21 2015] Beginning transcriptome assembly merge
-------------------------------------------
[Tue Sep  1 10:53:21 2015] Preparing output location ./merged_asm/
[Tue Sep  1 10:53:41 2015] Converting GTF files to SAM
[10:53:41] Loading reference annotation.
[10:53:45] Loading reference annotation.
[10:53:49] Loading reference annotation.
[10:53:53] Loading reference annotation.
[Tue Sep  1 10:53:58 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 /data/TAIR10_GFF3_genes_transposons.gff -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 8 ./merged_asm/tmp/mergeSam_fileg5BZPn
[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_fileg5BZPn doesn't appear to be a valid BAM file, trying SAM...
[10:53:58] Loading reference annotation.
[10:54:02] Inspecting reads and determining fragment length distribution.
Processed 30490 loci.                       
> Map Properties:
>       Normalized Map Mass: 166484.00
>       Raw Map Mass: 166484.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[10:54:05] Assembling transcripts and estimating abundances.
Processed 30490 loci.                       
[Tue Sep  1 10:54:44 2015] Comparing against reference file /data/TAIR10_GFF3_genes_transposons.gff
You are using Cufflinks v2.2.1, which is the most recent release.
[Tue Sep  1 10:55:03 2015] Comparing against reference file /data/TAIR10_GFF3_genes_transposons.gff
You are using Cufflinks v2.2.1, which is the most recent release.

 

cuffmerge cufflinks • 1.7k views
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