<p>There is a <a href="http://seqanswers.com/forums/showthread.php?t=39749" rel="nofollow noreferrer">post about this on seqanswers</a>. The poster says the following about cuffmerge behavior:</p>

<blockquote>
  <p>I kept the temporary files while running cuffmerge. It builgs a SAM file from transcripts.gtf files. Then it seems first it reads it as BAM since I read samtools take the files as BAM default. Then it finds it is not a BAM so it tries SAM. Then it can read it and resume the task. </p>
</blockquote>

<p>So it sounds like the BAM file is generated from GTF as a kludge inside cuffmerge, not the other way around. </p>

<p>Did you change any of the intermediate files or delete anything? Is there maybe a different cuffmerge run that it might be colliding with?</p>

<p>Did you get any output? it sounds like this error is frequently observed when actually the command completes fine, e.g. <a href="https://www.biostars.org/p/189139/" rel="nofollow noreferrer">https://www.biostars.org/p/189139/</a>. See other posts by googling the problem maybe, e.g. <a href="https://www.biostars.org/p/344439/" rel="nofollow noreferrer">https://www.biostars.org/p/344439/</a></p>

<p>(I know this isn't a proper answer but it was too involved for a comment.)</p>

CC BY-SA 4.0
2020-04-01T11:49:12.930Z
Thank you for your answer, No I did not delete anything and despite the warning the command was executed well.
Diango
CC BY-SA 4.0
2020-03-31T16:50:46.180Z
2020-03-31T16:50:46.180Z
Maximilian Press
<p>I need to merge my all transcripts.gtf from cufflinks output follow this command line :</p>
<pre><code>cuffmerge -o merged_gtf_output -p 15 -s ref.fasta -g anot.gtf assembly.txt
</code></pre>
<p>But I have this warning :</p>
<pre><code>[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 merge_B3//tmp/mergeSam_fileOaNffV doesn't appear to be a valid BAM file, trying SAM...
[21:40:04] Loading reference annotation.
[21:40:05] Inspecting reads and determining fragment length distribution.
Processed 3921 loci.                        
&gt; Map Properties:
&gt;       Normalized Map Mass: 33242.00
&gt;       Raw Map Mass: 33242.00
&gt;       Fragment Length Distribution: Truncated Gaussian (default)
&gt;                     Default Mean: 200
&gt;                  Default Std Dev: 80
</code></pre>
<p>Can someone tell me what this warning means and how to fix it?</p>

CC BY-SA 4.0
2020-03-29T11:26:12.750Z
it looks very weird to me, since you are not reading a bam file, some how samtools is called and it throws this warning, see also https://www.biostars.org/p/189139/
StupidWolf
CC BY-SA 4.0
2020-03-30T12:18:08.477Z
Yes it's true that it's weird, but I think it alludes to the files from which the gtf were generated by cufflinks
Diango
<rna-seq><samtools>
Cuffmerge: EOF marker is absent. The input is probably truncated
# Cuffmerge: EOF marker is absent. The input is probably truncated

(Asked by: username_0 on 2020-03-28)

I need to merge my all transcripts.gtf from cufflinks output follow this command line :
cuffmerge -o merged_gtf_output -p 15 -s ref.fasta -g anot.gtf assembly.txt

But I have this warning :
[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 merge_B3//tmp/mergeSam_fileOaNffV doesn't appear to be a valid BAM file, trying SAM...
[21:40:04] Loading reference annotation.
[21:40:05] Inspecting reads and determining fragment length distribution.
Processed 3921 loci.                        
> Map Properties:
>       Normalized Map Mass: 33242.00
>       Raw Map Mass: 33242.00
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80

Can someone tell me what this warning means and how to fix it?

**Tags:** rna-seq, samtools
> **Comments:**
> **username_1**: it looks very weird to me, since you are not reading a bam file, some how samtools is called and it throws this warning, see also https://www.biostars.org/p/189139/  
> **username_0**: Yes it's true that it's weird, but I think it alludes to the files from which the gtf were generated by cufflinks  

---

## 1 answers

### Answer by username_2 on 2020-03-31. Score: 1

There is a [post about this on seqanswers](http://seqanswers.com/forums/showthread.php?t=39749). The poster says the following about cuffmerge behavior:

> I kept the temporary files while running cuffmerge. It builgs a SAM file from transcripts.gtf files. Then it seems first it reads it as BAM since I read samtools take the files as BAM default. Then it finds it is not a BAM so it tries SAM. Then it can read it and resume the task.

So it sounds like the BAM file is generated from GTF as a kludge inside cuffmerge, not the other way around.

Did you change any of the intermediate files or delete anything? Is there maybe a different cuffmerge run that it might be colliding with?

Did you get any output? it sounds like this error is frequently observed when actually the command completes fine, e.g. <https://www.biostars.org/p/189139/>. See other posts by googling the problem maybe, e.g. <https://www.biostars.org/p/344439/>

(I know this isn't a proper answer but it was too involved for a comment.)

> **Comments:**
> **username_0**: Thank you for your answer, No I did not delete anything and despite the warning the command was executed well.  

---

