<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>

CC BY-SA 4.0
2020-03-03T18:53:15.050Z
Are you sure the parameters including word size and database, as well as all default settings are identical?
M__
CC BY-SA 4.0
2020-03-03T20:28:34.810Z
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).
Matteo Ferla
CC BY-SA 4.0
2020-03-04T09:29:28.690Z
@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...
Sofia
CC BY-SA 4.0
2020-03-04T10:28:49.273Z
@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?
Sofia
CC BY-SA 4.0
2020-03-04T15:11:34.993Z
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.
zorbax
CC BY-SA 4.0
2020-03-04T15:25:55.930Z
@zorbax, you don't need the option remote necessarily. also, what do you mean by "extra single quotation mark"
Sofia
CC BY-SA 4.0
2020-03-04T15:48:34.667Z
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.
zorbax
CC BY-SA 4.0
2020-03-04T16:08:53.650Z
If I add the remote option to my inital command, the result continues to be wrong...
Sofia
<blastn><windows>
Wrong blast results
# 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**: @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...  
> **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**: @zorbax, 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...  

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## 0 answers

