text: user15730: I am currently using VEP for variant annotation.
  I am facing an error as below:
  [E::fai_build_core] Different line length in sequence 'Pn9'
  
  I understand there is an issue with the difference in line length of Pn9 in the  fasta file. However, the sequences of fasta file all have different line length. I don't get why there is an error specifically on Pn9.
  I have tried using both snpEff and Annovar but doesn't work. Any thoughts on this would be really appreciated.
  I am attaching the length of sequence here :
  
  Thanks in advance.
  
  user73: This could be a bug in the fasta file reader component of fai_build_core. The fasta file format is very relaxed, and allows some odd constructions, for example:
  >cb3c6a5f-17dd-4cd6-a9ca-02124d2a32de
  AAGAAATTGACCTCCGTAACCCCAAAGGAGACAAAAAGAATGCTGGCTTTACTCCC
  CAGGAGCGCCAGGTTTTGGGGAACTGCCTACAAGCTGTACCATTGGCTGACAGCTT
  TTAGGGCATCTACCCCCAACACTGCTTACACTTACACTTTCTGGACTTACATG
  ATGAATGCCCGCTCTAAGAATGTTGGTTGGCGCCTTGATTACTTTTTGCTTTCC
  CACTCTCTTTTTACCTGCATTGTGACAGCAAGATCCGGTCAAGGCTCTTG
  GCAGTACACTGTCCCATCACCGCTACCTGTGATACCCCTCCCTGCAGTAGCTT
  CCTGCCTGGGAGATGGCTCTCTCTGCAGAAGTCTGGTGTTTTAGCC
  TTCAGGTGTTTGGTTTGTATGTGCTCCCTCATTTAAACATTAAACCAAACTT
  CTGGTTTCCTTTAGACAATCCAAGAGAAATAAAAGGCCCTAC
  TTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  
  A few programs will complain about fasta files that look like this, because it usually means that data has been corrupted. These programs only accept fasta files that have sequences with identical line lengths for all but the last line:
  >cb3c6a5f-17dd-4cd6-a9ca-02124d2a32de
  AAGAAATTGACCTCCGTAACCCCAAAGGAGACAAAAAGAATGCTGGCTTTACTCCC
  CAGGAGCGCCAGGTTTTGGGGAACTGCCTACAAGCTGTACCATTGGCTGACAGCTT
  TTAGGGCATCTACCCCCAACACTGCTTACACTTACACTTTCTGGACTTACATGATG
  AATGCCCGCTCTAAGAATGTTGGTTGGCGCCTTGATTACTTTTTGCTTTCCCACTC
  TCTTTTTACCTGCATTGTGACAGCAAGATCCGGTCAAGGCTCTTGGCAGTACACTG
  TCCCATCACCGCTACCTGTGATACCCCTCCCTGCAGTAGCTTCCTGCCTGGGAGAT
  GGCTCTCTCTGCAGAAGTCTGGTGTTTTAGCCTTCAGGTGTTTGGTTTGTATGTGC
  TCCCTCATTTAAACATTAAACCAAACTTCTGGTTTCCTTTAGACAATCCAAGAGAA
  ATAAAAGGCCCTACTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  
  One way to work around this input error problem is to get rid of all line breaks in the sequence of a fasta file, but then you run the risk of programs not properly being able to read all the characters in a line. A better approach is to feed the fasta file through a less restrictive data cleaning program and convert the lines back to all have a consistent length.
  There's a good chance this is not the problem you are experiencing, but without more information about your input data, all we have to go on are the error messages and the sequence lengths [not line lengths] you have provided.
  
original_text: 15730: <p>I am currently using VEP for variant annotation.</p>
  <p>I am facing an error as below:</p>
  <pre><code>[E::fai_build_core] Different line length in sequence 'Pn9'
  </code></pre>
  <p>I understand there is an issue with the difference in line length of Pn9 in the  fasta file. However, the sequences of fasta file all have different line length. I don't get why there is an error specifically on Pn9.</p>
  <p>I have tried using both snpEff and Annovar but doesn't work. Any thoughts on this would be really appreciated.</p>
  <p>I am attaching the length of sequence here :
  <img src="https://i.stack.imgur.com/6xMuH.jpg" alt="length per chromosome" /></p>
  <p>Thanks in advance.</p>
   73: <p>This could be a bug in the fasta file reader component of fai_build_core. The fasta file format is very relaxed, and allows some odd constructions, for example:</p>
  <pre><code>&gt;cb3c6a5f-17dd-4cd6-a9ca-02124d2a32de
  AAGAAATTGACCTCCGTAACCCCAAAGGAGACAAAAAGAATGCTGGCTTTACTCCC
  CAGGAGCGCCAGGTTTTGGGGAACTGCCTACAAGCTGTACCATTGGCTGACAGCTT
  TTAGGGCATCTACCCCCAACACTGCTTACACTTACACTTTCTGGACTTACATG
  ATGAATGCCCGCTCTAAGAATGTTGGTTGGCGCCTTGATTACTTTTTGCTTTCC
  CACTCTCTTTTTACCTGCATTGTGACAGCAAGATCCGGTCAAGGCTCTTG
  GCAGTACACTGTCCCATCACCGCTACCTGTGATACCCCTCCCTGCAGTAGCTT
  CCTGCCTGGGAGATGGCTCTCTCTGCAGAAGTCTGGTGTTTTAGCC
  TTCAGGTGTTTGGTTTGTATGTGCTCCCTCATTTAAACATTAAACCAAACTT
  CTGGTTTCCTTTAGACAATCCAAGAGAAATAAAAGGCCCTAC
  TTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  </code></pre>
  <p>A few programs will complain about fasta files that look like this, because it usually means that data has been corrupted. These programs only accept fasta files that have sequences with identical line lengths for all but the last line:</p>
  <pre><code>&gt;cb3c6a5f-17dd-4cd6-a9ca-02124d2a32de
  AAGAAATTGACCTCCGTAACCCCAAAGGAGACAAAAAGAATGCTGGCTTTACTCCC
  CAGGAGCGCCAGGTTTTGGGGAACTGCCTACAAGCTGTACCATTGGCTGACAGCTT
  TTAGGGCATCTACCCCCAACACTGCTTACACTTACACTTTCTGGACTTACATGATG
  AATGCCCGCTCTAAGAATGTTGGTTGGCGCCTTGATTACTTTTTGCTTTCCCACTC
  TCTTTTTACCTGCATTGTGACAGCAAGATCCGGTCAAGGCTCTTGGCAGTACACTG
  TCCCATCACCGCTACCTGTGATACCCCTCCCTGCAGTAGCTTCCTGCCTGGGAGAT
  GGCTCTCTCTGCAGAAGTCTGGTGTTTTAGCCTTCAGGTGTTTGGTTTGTATGTGC
  TCCCTCATTTAAACATTAAACCAAACTTCTGGTTTCCTTTAGACAATCCAAGAGAA
  ATAAAAGGCCCTACTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
  </code></pre>
  <p>One way to work around this input error problem is to get rid of <em>all</em> line breaks in the sequence of a fasta file, but then you run the risk of programs not properly being able to read all the characters in a line. A better approach is to feed the fasta file through a less restrictive data cleaning program and convert the lines back to all have a consistent length.</p>
  <p>There's a good chance this is <em>not</em> the problem you are experiencing, but without more information about your input data, all we have to go on are the error messages and the sequence lengths [not line lengths] you have provided.</p>
  