Question: Cuffmerge BAM error
0
gravatar for jenkelly
3.4 years ago by
jenkelly0
jenkelly0 wrote:

Dear forum

I have run cuffmerge on multiple gtf files generated by cufflinks. I am getting the following 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 cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/tmp/mergeSam_fileMhPT93 doesn't appear to be a valid BAM file, trying SAM...

but it seems to complete ok, and produces a merged.gtf file at the end. Is this running correctly or is there something wrong with the input gtf files? (see full output below)

Thank you for your help, Kate

[

Thu Apr 28 11:34:15 2016] Preparing output location cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/
[Thu Apr 28 11:34:19 2016] Converting GTF files to SAM
[11:34:19] Loading reference annotation.
[11:34:21] Loading reference annotation.
[11:34:23] Loading reference annotation.
[11:34:25] Loading reference annotation.
[11:34:26] Loading reference annotation.
[Thu Apr 28 11:34:29 2016] Quantitating transcripts
You are using Cufflinks v2.2.1, which is the most recent release.
Command line:
cufflinks -o cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/ -F 0.05 -g ref_genomes/Oncorhynchus_mykiss_chr_annot_rename_sort.gtf -q --overhang-tolerance 200 --library-type=transfrags -A 0.0 --min-frags-per-transfrag 0 --no-5-extend -p 16 cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/tmp/mergeSam_fileMhPT93 
[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 cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge/tmp/mergeSam_fileMhPT93 doesn't appear to be a valid BAM file, trying SAM...
[11:34:29] Loading reference annotation.
[11:34:32] Inspecting reads and determining fragment length distribution.
Processed 44693 loci.                       
> Map Properties:
>   Normalized Map Mass: 232925.00
>   Raw Map Mass: 232925.00
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
[11:34:34] Assembling transcripts and estimating abundances.
Processed 44693 loci.                       
[Thu Apr 28 11:35:44 2016] Comparing against reference file ref_genomes/Oncorhynchus_mykiss_chr_annot_rename_sort.gtf
You are using Cufflinks v2.2.1, which is the most recent release.
[Thu Apr 28 11:36:06 2016] Comparing against reference file ref_genomes/Oncorhynchus_mykiss_chr_annot_rename_sort.gtf
You are using Cufflinks v2.2.1, which is the most recent release.

rna-seq error cuffmerge bam • 1.7k views
ADD COMMENTlink written 3.4 years ago by jenkelly0

It seems to complain about the bam file, which is probably not a bam file but a sam file.

Did you use a sam file instead of bam? If so, the program automatically tried sam after it discovered it was not a bam (I don't know if this is a real error, seems more like a warning).

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Benn7.7k

Sorry I should have also posted the command I used:

cuffmerge -p 16 -o cufflinks_frsecondstrand/cuffmerge/trout_cuffmerge -g ref_genomes/Oncorhynchus_mykiss_chr_annot_rename_sort.gtf -s ref_genomes/bowtie_index/rainbow_trout.fa cufflinks_frsecondstrand/cuffmerge/trout_gft_list.txt

As you can see there was no BAM or SAM given as an input file.

ADD REPLYlink written 3.4 years ago by jenkelly0

You're right, there is no sam or bam file needed for cuffmerge. I don't know why it is complaining about it.

You say that you get right results, so I would ignore the warning about the bam and sam files...

ADD REPLYlink written 3.4 years ago by Benn7.7k
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