Error using matlab.int​ernal.webs​ervices.HT​TPConnecto​r/copyCont​entToByteA​rray (line 396) The server returned the status 429 with message "Too Many Requests" in response to the request to URL.

I am writing a script that will take my protein sequence of interest and find matches to it using NCBI blast. I identify the hits and then try and get the sequence for each (in code this is 'j=1:.....'). This works fine, but when I get to number 1226, I get the error below. I have tried a couple of things:

• Pausing longer between iterations of my loop did not help
• Manually doing this particular one in the command window returned the same error, though if I go to the NCBI website and find the protein, there's no problem.

Any advice would be greatly appreciated!!

THE ERROR:

Error using matlab.internal.webservices.HTTPConnector/copyContentToByteArray

(line 396)

The server returned the status 429 with message "Too Many Requests" in response

to the request to URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nucest&term=NXO81641%5BAccession%5D.

Error in readContentFromWebService (line 46)

byteArray = copyContentToByteArray(connection);

Error in webread (line 125)

[varargout{1:nargout}] = readContentFromWebService(connection, options);

Error in getncbidata>accession2gi (line 316)

searchXML = webread(searchurl);

Error in getncbidata (line 182)

[giID,db] = accession2gi(accessnum,db,'quick');

Error in getgenpept (line 64)

[varargout{1:nargout}] =

getncbidata(accessnum,'database','protein','fileformat','GenPept',varargin{:});

75 rethrow(e)

MY CODE:

%% Get a list of everything that aligns with TPC2 (and must be listed as TPC2)
 
POI = 'MAEPQAESEPLLGGARGGGGDWPAGLTTYRSIQVGPGAAARWDLCIDQAVVFIEDAIQYRSINHRVDASSMWLYRRYYSNVCQRTLSFTIFLILFLAFIETPSSLTSTADVRYRAAPWEPPCGLTESVEVLCLLVFAADLSVKGYLFGWAHFQKNLWLLGYLVVLVVSLVDWTVSLSLVCHEPLRIRRLLRPFFLLQNSSMMKKTLKCIRWSLPEMASVGLLLAIHLCLFTMFGMLLFAGGKQDDGQDRERLTYFQNLPESLTSLLVLLTTANNPDVMIPAYSKNRAYAIFFIVFTVIGSLFLMNLLTAIIYSQFRGYLMKSLQTSLFRRRLGTRAAFEVLSSMVGEGGAFPQAVGVKPQNLLQVLQKVQLDSSHKQAMMEKVRSYGSVLLSAEEFQKLFNELDRSVVKEHPPRPEYQSPFLQSAQFLFGHYYFDYLGNLIALANLVSICVFLVLDADVLPAERDDFILGILNCVFIVYYLLEMLLKVFALGLRGYLSYPSNVFDGLLTVVLLVLEISTLAVYRLPHPGWRPEMVGLLSLWDMTRMLNMLIVFRFLRIIPSMKLMAVVASTVLGLVQNMRAFGGILVVVYYVFAIIGINLFRGVIVALPGNSSLAPANGSAPCGSFEQLEYWANNFDDFAAALVTLWNLMVVNNWQVFLDAYRRYSGPWSKIYFVLWWLVSSVIWVNLFLALILENFLHKWDPRSHLQPLAGTPEATYQMTVELLFRDILEEPGEDELTERLSQHPHLWLCR'

%Blast the inputted sequence against NCBI protein. Return 5000 results. 
[blastsend, waittime]=blastncbi(POI, 'blastp', 'MaxNumberSequences', 5000);
 
%Get a copy of the blast report. 
tm = string(datetime('now'));
blastresultsfile=string('blastresults'+tm+'.xml');
getblast(blastsend, 'Wait', waittime, 'ToFile', blastresultsfile);
%%
%Read in the blast results.
BlastFile=blastread('blastresults.xml');
BlastFileTb=struct2table(BlastFile.Hits);

IdentityFile=strings(1);
%Get the Identity value!
for b=1:height(BlastFileTb)
    
   
    
    IdentityFile(1,b)=((BlastFile.Hits(b).Hsps(1).Identities)/752)*100;
   
end

IdentityFile=IdentityFile';
%Identify the different elements of the blast report. 
Definition=table(BlastFileTb.Definition);
Definition.Properties.VariableNames={'Definition'};
ID=table(BlastFileTb.ID);
ID.Properties.VariableNames={'ID'};
Accession=table(BlastFileTb.Accession);
Accession.Properties.VariableNames={'Accession'};
Identity=table(IdentityFile);
Identity.Properties.VariableNames={'Identity'};
ExtractedBlast=[ID, Definition, Accession, Identity];
%%

TPC2_list1=ExtractedBlast(contains(ExtractedBlast.Definition, 'protein 2'),:);
TPC2_list2=ExtractedBlast(contains(ExtractedBlast.Definition, 'TPC2'),:);
TPC2_totallist=[TPC2_list1;TPC2_list2];


specieslist=strings(1);
seqlist=strings(1);
%%

% Now we have a list of all the TPC2 on ncbi. I want to identify a) all the
% the speices wirth it and b) also be ab;e to check box the species I want
% to focus on.

for i=1:height(TPC2_totallist)
    
    %Take the description of the target
    thisentry=string(table2array(TPC2_totallist(i,2)));
    
 %Find the name of the species by looking between square brackets
   findingspecies=split(thisentry, '[');
   findingspecies2=findingspecies(contains(findingspecies, ']'));
   findingspecies3= split(findingspecies2(1), ']') ;
   speciesname=findingspecies3(1);
   
   %Make a list of all the species
    specieslist(i,1)=speciesname;
    
    %Remove any repeats from the species list.
    unique_specieslist=unique(specieslist);
    
end
%    
%% 
%Add the species list to the table we've been working from
TPC2_amendedlist=[TPC2_totallist, array2table(specieslist)];
%%
%% **THIS IS WHERE I HAVE THE PROBLEM, WITH NUMBER 1226
for j=1:height(TPC2_amendedlist)
    %For each entry, get the accession number
    accno=string(table2array(TPC2_amendedlist(j,3)));
    
    %Use the accession number to get the FASTA online. Put it in a list for
    %now ('seqlist')
    seq=getgenpept(accno, 'SequenceOnly', true) ;
    seqlist(1,j)=seq;
    %This step needs a pause ( 1 sec) because the server will ping too often if not
    %and reject the request. An extra pause on every tenth iteration.  'j' indicates what iteration we're on. 
    j
    pause(.5);
   % if mod(j, 10)==0
      %  pause(10);
   % end
end

Answer 1

[Tarunbir Gambhir]

I tried to execute your code and got a similar error stacktrace, after retrieving 331 sequences. The problem is as described in the error description, it is a restriction at the NCBI server and nothing wrong with your script.

For your case, I would suggest to try and break up the work into segments of 1225 sequences each and run the script again for each segment. I understand this is not a solution, but it might be a workaround to your problem.