Body: <p>During <a href="https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=1d92ebdf7e8d466c&amp;tool_config=%2Fsrv%2Ftoolshed-repos%2Fmain%2F000%2Frepo_241%2Ftools%2Fncbi_blast_plus%2Fncbi_segmasker_wrapper.xml&amp;changeset_revision=5edc472ec434" rel="nofollow noreferrer">NCBI BLAST+ segmasker</a> output exploration, I found out that for some sequences, the program returns the same interval twice:</p>
  <pre><code>&gt;tr|A0A0D2B4V6|A0A0D2B4V6_9EURO Uncharacterized protein OS=Cladophialophora immunda OX=569365 GN=PV07_04097 PE=3 SV=1
  131 - 139
  131 - 139
  </code></pre>
  <p>This seems not to be a planned behaviour, but maybe someone has an explanation.</p>
  <p>The command I ran was:</p>
  <pre><code>segmasker -in &lt;input_file&gt; -out &lt;output_file&gt; -locut 1.5 -hicut 1.8 -window 15
  </code></pre>
  <hr />
  <p>Exemplary sequences triggering such an event:</p>
  <pre><code>&gt;sequence1
  MDSHNSSTLIILSLPPKTFVGLDLVSFDSSPNFQGIAKIPVGIHFLYTGTDASLSIRHGRWLNLTSTHPIQVLRWNSDGETLQPVDQNDQTARNAIAAISNGRGLVDYGALQSATSELSTRESQSHDASSLAAAAAAAAADEDRAESTDWPALTAHISSPLLTRILSPDWIVSSISSAPTDTETIPGLSHLEASNALHQLPLDLLPVNLKQTWAGGDIGRARTERARDRSWYLGQLIEQAARPQGGDKTAGAREVLGELQFCFLMVLTLANYSCLEQWKRLLSVFFTCRTALDEVEGYFVQVIRVLRLQIKHVDDVEGGLFELRDESGSAWLRTLWARFRSVVDDADKGERVSLKKEVDALEKLFEGKYGWQSERDILRRGMLELEDGERVEVTMHGVDEDEETGEYAPVIVET
  &gt;sequence2
  VDKLFKKNAMGNNIFHEIAIQGSLMLLQTIRDNVDGQMDTYLSEINDQNESCITIVADRHRGLLAKDLIEIFVDLGADINETDNWGNTALHYSVFHRDHVLAEWLCQQPGINLNAINNDEHTPLGLAILWNIQSIKTLLESKGARFNNIEFSDSETSDDDDDDDDDGHDENDE
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-28T16:52:07.330Z
Comments.Text: What command are you running? What options?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-28T20:27:55.807Z
Comments.Text: Right, I should have include it. `segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15`.
Comments.UserDisplayName: maciejwww
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-29T19:13:48.740Z
Comments.Text: Could there be something silly like having duplicate sequences in your input? Which are then combined in the output?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-29T21:30:38.517Z
Comments.Text: Nah, I've just run *segmasker* on the given example and [got](https://pastebin.pl/view/675aabe7).
Comments.UserDisplayName: maciejwww
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-11-29T21:31:21.340Z
Comments.Text: I'm using *segmasker* locally. Installed last week.
Comments.UserDisplayName: maciejwww
Tags: <phylogenetics><segmasker><bugs>
Title: segmasker doubles found intervals
ThreadText: # segmasker doubles found intervals
  
  (Asked by: username_0 on 2022-11-26)
  
  During [NCBI BLAST+ segmasker](https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=1d92ebdf7e8d466c&tool_config=%2Fsrv%2Ftoolshed-repos%2Fmain%2F000%2Frepo_241%2Ftools%2Fncbi_blast_plus%2Fncbi_segmasker_wrapper.xml&changeset_revision=5edc472ec434) output exploration, I found out that for some sequences, the program returns the same interval twice:
  
  ```
  >tr|A0A0D2B4V6|A0A0D2B4V6_9EURO Uncharacterized protein OS=Cladophialophora immunda OX=569365 GN=PV07_04097 PE=3 SV=1
  131 - 139
  131 - 139
  
  ```
  
  This seems not to be a planned behaviour, but maybe someone has an explanation.
  
  The command I ran was:
  
  ```
  segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15
  
  ```
  
  ---
  
  Exemplary sequences triggering such an event:
  
  ```
  >sequence1
  MDSHNSSTLIILSLPPKTFVGLDLVSFDSSPNFQGIAKIPVGIHFLYTGTDASLSIRHGRWLNLTSTHPIQVLRWNSDGETLQPVDQNDQTARNAIAAISNGRGLVDYGALQSATSELSTRESQSHDASSLAAAAAAAAADEDRAESTDWPALTAHISSPLLTRILSPDWIVSSISSAPTDTETIPGLSHLEASNALHQLPLDLLPVNLKQTWAGGDIGRARTERARDRSWYLGQLIEQAARPQGGDKTAGAREVLGELQFCFLMVLTLANYSCLEQWKRLLSVFFTCRTALDEVEGYFVQVIRVLRLQIKHVDDVEGGLFELRDESGSAWLRTLWARFRSVVDDADKGERVSLKKEVDALEKLFEGKYGWQSERDILRRGMLELEDGERVEVTMHGVDEDEETGEYAPVIVET
  >sequence2
  VDKLFKKNAMGNNIFHEIAIQGSLMLLQTIRDNVDGQMDTYLSEINDQNESCITIVADRHRGLLAKDLIEIFVDLGADINETDNWGNTALHYSVFHRDHVLAEWLCQQPGINLNAINNDEHTPLGLAILWNIQSIKTLLESKGARFNNIEFSDSETSDDDDDDDDDGHDENDE
  
  ```
  
  **Tags:** phylogenetics, segmasker, bugs
  
  > **Comments:**
  > **username_1**: What command are you running? What options?  
  > **username_0**: Right, I should have include it. `segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15`.  
  > **username_1**: Could there be something silly like having duplicate sequences in your input? Which are then combined in the output?  
  > **username_0**: Nah, I've just run *segmasker* on the given example and [got](https://pastebin.pl/view/675aabe7).  
  > **username_0**: I'm using *segmasker* locally. Installed last week.  
  
  ---
  
  ## 0 answers
  
  