<p>Hello,</p>

<p>I have been trying the last days to make my database for blast work but I really don&#39;t know how to figure out this problem.</p>

<p>Begining from the start of the problem, I want to make a blastp against a protein database that I have created.</p>

<p>Here is an example of my sequence identifiers and how they are formatted:</p>

<p><strong>&gt;TRA_G345655|locus=scaffold45|99209|101155|-|translate_table|standard</strong></p>

<p>I try to make the blast database with the following command:</p>

<p><strong>makeblastdb -in database.fa -title database -dbtype prot -out protdb -parse_seqids</strong></p>

<p>It does not work and it gives me the following error:</p>

<p><strong>No volumes were created because no sequences were found.</strong></p>

<p><strong>BLAST Database creation error: Defline lacks a proper ID around line 1</strong></p>

<p>When I try it without &#39;-parse_seqids&#39;, it works fine and it generated the three files with pin, psq and phr.</p>

<p>I put these 3 files with my database.fa fasta file in one folder called DB and then I try to run blastp with the following command:</p>

<p><strong>blastp -query query.fa -db DB -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6</strong></p>

<p>or with:</p>

<p><strong>blastp -query query.fa -db DB/database.fa -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6</strong></p>

<p>or with:</p>

<p><strong>blastp -query query.fa -db database -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6</strong></p>

<p>But it gives me the following error:</p>

<p><strong>BLAST Database error: No alias or index file found for protein database [database] in search path</strong></p>

<p>How can I solve this problem or where is the origin of this problem?</p>

The documentation on how to build proper sequence ids is [here][1]

 [1]: http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_demo/#ch_demo.T5

In short: your fasta defline doesn't contain a valid identifier and needs to be changed to be parsable. A valid identifier consists of two or three fields separated by `|`.

E.g. for a ref seq entry:

    ref|NM_010450.1|

For your case most likely the sequence has a local identifier, then you should change your defline to start with:

    lcl|TRA_G345655

The second error is caused by:

    makeblastdb -in database.fa -title database -dbtype prot -out protdb -parse_seqids

**so you also need to change this**:

    blastp -query query.fa -db protdb -out proteins_blastp_1e-30_table.txt -evalue 1e-30 -outfmt 6