I am trying to run the program here:
http://dasan.sejong.ac.kr/~wikim/notice.html
In one of the .java files, it makes a call to the blastp function in the NCBI blast+ package.
public ArrayList runBlast(String query, String subject) {
ArrayList scoreList = new ArrayList();
Runtime rt = Runtime.getRuntime();
subject = ParaNames.Species+subject;
try {
Process proc = rt.exec(new String[] {"~/Downloads/ncbi-blast-2.2.30+/bin/blastp", "-query", query, "-subject", subject, "-num_threads", "4", "-matrix", matrix, "-outfmt", "10 qseqid sseqid score"});
InputStream is = proc.getInputStream();
InputStream es = proc.getErrorStream();
BufferedReader reader = new BufferedReader(new InputStreamReader(is));
BufferedReader readerError = new BufferedReader(new InputStreamReader(es));
String line;
while ((line = reader.readLine()) != null) {
scoreList.add(line);
}
if (proc.waitFor() != 0) {
System.err.println("Process exited with (normal termination: 0) "+proc.exitValue());
System.err.println("Error: "+readerError.readLine());
}
is.close(); is = null;
es.close(); es = null;
reader.close(); reader = null;
readerError.close(); readerError = null;
proc.destroy(); proc = null;
}
catch (InterruptedException e) {
System.err.println("Error: "+e.getMessage());
}
catch (IOException ioe) {
System.err.println("Failed to execute: "+ioe.getMessage());
}
return scoreList;
}
I have downloaded ncbi-blast-2.2.30+ and it is in the Downloads folder.
When I run this however, I am getting the following error:
May 20, 2015 1:40:33 PM ReMark.RecursiveClustering <init>
INFO: Trying to run BLAST now - this may take several hours ... or days!
May 20, 2015 1:40:33 PM ReMark.RecursiveClustering <init>
INFO: Starting ortholog detection...................................
Failed to execute: Cannot run program "~/Downloads/ncbi-blast-2.2.30+/bin/blast": error=2, No such file or directory
Failed to execute: Cannot run program "~/Downloads/ncbi-blast-2.2.30+/bin/blast": error=2, No such file or directory
Failed to execute: Cannot run program "~/Downloads/ncbi-blast-2.2.30+/bin/blast": error=2, No such file or directory
Failed to execute: Cannot run program "~/Downloads/ncbi-blast-2.2.30+/bin/blast": error=2, No such file or directory
Failed to execute: Cannot run program "~/Downloads/ncbi-blast-2.2.30+/bin/blast": error=2, No such file or directory
Could someone explain what I need to do to fix this? I can provide any other information you need. Thank you very much.
Looks like it is looking for
blastexecutable instead ofblastp.Does that program requires legacy blast (non-plus version)?I don't think so, because originally it just said "blastp" where it is currently written "~/Downloads/ncbi-blast-2.2.30+/bin/blastp"