text: user6694: 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?
  
  user2108: There is a post about this on seqanswers. 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.)
  
original_text: 6694: <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>
   2108: <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>
  