Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-01T11:49:12.930Z
Answers.Text: Thank you for your answer, No I did not delete anything and despite the warning the command was executed well.
Answers.UserDisplayName: Diango
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-31T16:50:46.180Z
Answers.LastActivityDate: 2020-03-31T16:50:46.180Z
Answers.UserDisplayName: Maximilian Press
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-29T11:26:12.750Z
Comments.Text: 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/
Comments.UserDisplayName: StupidWolf
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-30T12:18:08.477Z
Comments.Text: Yes it's true that it's weird, but I think it alludes to the files from which the gtf were generated by cufflinks
Comments.UserDisplayName: Diango
Tags: <rna-seq><samtools>
Title: Cuffmerge: EOF marker is absent. The input is probably truncated
ThreadText: # 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.  
  
  ---
  
  