<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>

CC BY-SA 4.0
2022-11-28T16:52:07.330Z
What command are you running? What options?
terdon
CC BY-SA 4.0
2022-11-28T20:27:55.807Z
Right, I should have include it. `segmasker -in <input_file> -out <output_file> -locut 1.5 -hicut 1.8 -window 15`.
maciejwww
CC BY-SA 4.0
2022-11-29T19:13:48.740Z
Could there be something silly like having duplicate sequences in your input? Which are then combined in the output?
terdon
CC BY-SA 4.0
2022-11-29T21:30:38.517Z
Nah, I've just run *segmasker* on the given example and [got](https://pastebin.pl/view/675aabe7).
maciejwww
CC BY-SA 4.0
2022-11-29T21:31:21.340Z
I'm using *segmasker* locally. Installed last week.
maciejwww
<phylogenetics><segmasker><bugs>
segmasker doubles found intervals
# segmasker doubles found intervals

(Asked by: username_0 on 2022-11-26)

During NCBI BLAST+ segmasker 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  -out  -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

