<p>Try with:</p>

<pre><code>makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90
</code></pre>

<p>The <code>-out</code> is the name of the DB. So if you use <code>uniref90.fasta</code>, it creates <code></code>uniref90.fasta.pin<code>while the script seems to be expecting</code>uniref90.pin`.</p>

CC BY-SA 4.0
2018-07-11T13:23:46.740Z
2018-07-12T08:27:51.123Z
2018-07-12T08:27:51.123Z
h.mon
<p>I am trying to install psipred in a unix server.</p>

<p>Psipred is installed, but fails because it can not find the correct database files.  I have downloaded uniprod90.fasta. Psipred also loads the old legacy ncbi BLAST-2.2.26 and BLAST+.<br>
<code>runpsipred</code> and <code>runpsipredplus</code> have been patched to call the correct version of BLAST. </p>

<p>I have run a few commands to index the uniprod90 database: </p>

<pre><code>pfilt uniref90.fasta &gt; uniref90filt
formatdb -t uniref90filt -i uniref90filt
makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta
</code></pre>

<p>I then ran <code>psipred</code> and got this error:</p>

<pre><code>$ ./psipred/example/example.fasta
Running PSI-BLAST with sequence  ./psipred/example/example.fasta ...
[blastpgp] WARNING: Unable to open uniref90.pin
[blastpgp] WARNING: Unable to open uniref90.pin
FATAL: Error whilst running blastpgp - script terminated!
</code></pre>

<p><code>makeblastdb</code> created 26 pin files, but not uniref90.pin.</p>

<software-installation>
Psipred installation
# Psipred installation

(Asked by: username_0 on 2018-07-10)

I am trying to install psipred in a unix server.
Psipred is installed, but fails because it can not find the correct database files.  I have downloaded uniprod90.fasta. Psipred also loads the old legacy ncbi BLAST-2.2.26 and BLAST+.
runpsipred and runpsipredplus have been patched to call the correct version of BLAST. 
I have run a few commands to index the uniprod90 database: 
pfilt uniref90.fasta > uniref90filt
formatdb -t uniref90filt -i uniref90filt
makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90.fasta

I then ran psipred and got this error:
$ ./psipred/example/example.fasta
Running PSI-BLAST with sequence  ./psipred/example/example.fasta ...
[blastpgp] WARNING: Unable to open uniref90.pin
[blastpgp] WARNING: Unable to open uniref90.pin
FATAL: Error whilst running blastpgp - script terminated!

makeblastdb created 26 pin files, but not uniref90.pin.

**Tags:** software-installation

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## 1 answers

### Answer by username_1 on 2018-07-11. Score: 4 | Accepted answer

Try with:
makeblastdb -in uniref90.fasta -dbtype prot -input_type fasta -out uniref90

The -out is the name of the DB. So if you use uniref90.fasta, it creates uniref90.fasta.pinwhile the script seems to be expectinguniref90.pin`.


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