Body: <p>I'm sorry if this is a naive question, but I get an odd thing going on.
  I'm performing blast remotely in this way: </p>
  
  <pre><code>'blastn -task megablast -outfmt "6 std ssciname" -reward 1 -penalty -3  -db nt_v5 -max_target_seqs 100 -word_size 22 -query ' + final_file + " -taxidlist " + Plants_DB + " -out " + blastfile
  </code></pre>
  
  <p>However, when I see my remote results, I get a species whose seqid gives me <em>Vaccinium oxycoccos</em>. And when I put this seqid in blast online, the species is totally different. </p>
  
  <p>(With this blast command, I perform a blast search against a specific list of IDS.) </p>
  
  <p>How can this happen?</p>
  
  <p>Thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-03T18:53:15.050Z
Comments.Text: Are you sure the parameters including word size and database, as well as all default settings are identical?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-03T20:28:34.810Z
Comments.Text: What exactly do you mean by seqid? Species have taxid, e.g. humans are 9606. Whereas genbank files have accession numbers (and formerly gi numbers).
Comments.UserDisplayName: Matteo Ferla
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T09:29:28.690Z
Comments.Text: @MatteoFerla I have this result, 4F703:00578:02013 KX677575.1 100.000 320 0 0 1 320 700 381 3.25e-165 592 Vaccinium oxycoccos and when I put the second result in blast I get a different specie...
Comments.UserDisplayName: Sofia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T10:28:49.273Z
Comments.Text: @MichaeG. I tried to specify the most part with this commands: blastn -task megablast -word_size 28 -reward 1 -penalty -2 -outfmt 6 std ssciname -db nt_v5 -max_target_seqs 100 -query input.fasta -taxidlist test_ID_plants.ids -out blastfile.txt... do you think there is a problem with my nt database?
Comments.UserDisplayName: Sofia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T15:11:34.993Z
Comments.Text: what do you mean with remotely? because in your command you are not using the `--remote` option, and there is an extra single quotation mark as well.
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T15:25:55.930Z
Comments.Text: @zorbax, you don't need the option remote necessarily. also, what do you mean by "extra single quotation mark"
Comments.UserDisplayName: Sofia
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T15:48:34.667Z
Comments.Text: I assume that you call "remotely" because you are running your process in a remote computer. But the `-remote` option in blast means remote service at the NCBI servers, otherwise you are using a local version of nt database called nt_v5.
Comments.UserDisplayName: zorbax
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-03-04T16:08:53.650Z
Comments.Text: If I add the remote option to my inital command, the result continues to be wrong...
Comments.UserDisplayName: Sofia
Tags: <blastn><windows>
Title: Wrong blast results
ThreadText: # Wrong blast results
  
  (Asked by: username_0 on 2020-03-03)
  
  I'm sorry if this is a naive question, but I get an odd thing going on.
  I'm performing blast remotely in this way:
  
  ```
  'blastn -task megablast -outfmt "6 std ssciname" -reward 1 -penalty -3  -db nt_v5 -max_target_seqs 100 -word_size 22 -query ' + final_file + " -taxidlist " + Plants_DB + " -out " + blastfile
  
  ```
  
  However, when I see my remote results, I get a species whose seqid gives me *Vaccinium oxycoccos*. And when I put this seqid in blast online, the species is totally different.
  
  (With this blast command, I perform a blast search against a specific list of IDS.)
  
  How can this happen?
  
  Thanks
  
  **Tags:** blastn, windows
  
  > **Comments:**
  > **username_1**: Are you sure the parameters including word size and database, as well as all default settings are identical?  
  > **username_2**: What exactly do you mean by seqid? Species have taxid, e.g. humans are 9606. Whereas genbank files have accession numbers (and formerly gi numbers).  
  > **username_0**: @username_2 I have this result, 4F703:00578:02013 KX677575.1 100.000 320 0 0 1 320 700 381 3.25e-165 592 Vaccinium oxycoccos and when I put the second result in blast I get a different specie...  
  > **username_0**: @MichaeG. I tried to specify the most part with this commands: blastn -task megablast -word_size 28 -reward 1 -penalty -2 -outfmt 6 std ssciname -db nt_v5 -max_target_seqs 100 -query input.fasta -taxidlist test_ID_plants.ids -out blastfile.txt... do you think there is a problem with my nt database?  
  > **username_3**: what do you mean with remotely? because in your command you are not using the `--remote` option, and there is an extra single quotation mark as well.  
  > **username_0**: @username_3, you don't need the option remote necessarily. also, what do you mean by "extra single quotation mark"  
  > **username_3**: I assume that you call "remotely" because you are running your process in a remote computer. But the `-remote` option in blast means remote service at the NCBI servers, otherwise you are using a local version of nt database called nt_v5.  
  > **username_0**: If I add the remote option to my inital command, the result continues to be wrong...  
  
  ---
  
  ## 0 answers
  
  