<p>The easiest solution is to install miniconda and then install via mamba</p>
<pre><code>mamba create --name myenvname blast
mamba activate blast
mamba install blast
mamba update blast
blastn -query /staging/Blast/Input/HBV/Sample1.seq.fasta -db /tmp/ramdisk_prok/nt_prok -task blastn -evalue 1e-6 -max_hsps 1 -max_target_seqs 500 -outfmt &quot;6 qseqid qlen qstart qend sseqid slen sstart send length nident pident mismatch gaps gapopen qcovs evalue bitscore stitle sskingdoms staxids sscinames sblastnames qseq sseq&quot; -num_threads 10 -out /staging/Blast/Output/HBV/Sample1.original.txt
mamba deactivate
</code></pre>
<p><strong>Check</strong>
Do you have io permission for</p>
<pre><code>/staging/Blast/Input/HBV/Sample1.seq.fasta
/staging/Blast/Output/HBV/Sample1.original.txt
</code></pre>
<hr />
<p>To install mamba you'll need Anaconda because its within the <a href="https://anaconda.org/bioconda/sra-tools" rel="nofollow noreferrer">Anaconda collection</a> and simplifies everything on three counts, viz:</p>
<ul>
<li>in answer to your question all configurations are automated</li>
<li>it is easy to automate all updates</li>
<li>it offers a virtual environment where code can't mess with your system</li>
<li>whenever you want to download other packages its the same approach</li>
</ul>
<p>Thus all you have to do is download and install <a href="https://www.anaconda.com/products/individual" rel="nofollow noreferrer">Anaconda</a> or <a href="https://docs.conda.io/en/latest/miniconda.html" rel="nofollow noreferrer">miniconda</a>. From this point everything is done using conda, either:</p>
<p>Anaconda installs in two different locations depending on whether you install the GUI version, which makes maintenance and environments a bit easier. In the later case I think its <code>/opt</code>, otherwise the commandline version is <code>~/anadonda3</code>.</p>
<p>Thereon,</p>
<pre><code>conda config --add channels conda-forge
conda update -n base --all
conda install -n base mamba
</code></pre>

CC BY-SA 4.0
2024-06-01T15:20:31.440Z
2024-06-01T15:20:31.440Z
M__
<p>I have created a database and added environment variables, but an &quot;error message&quot; still appears. How can I solve it?</p>
<pre><code>error message: BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/Tina:/tmp/ramdisk_prok:]
</code></pre>
<p><em>Blast Database</em></p>
<pre><code>$ cd /tmp/ramdisk_prok

    nt_prok.00.nhr  nt_prok.04.nnd  nt_prok.08.nog  nt_prok.13.nhr  nt_prok.17.nnd
    nt_prok.00.nin  nt_prok.04.nni  nt_prok.08.nsq  nt_prok.13.nin  nt_prok.17.nni
    nt_prok.00.nnd  nt_prok.04.nog  nt_prok.09.nhr  nt_prok.13.nnd  nt_prok.17.nog
    nt_prok.00.nni  nt_prok.04.nsq  nt_prok.09.nin  nt_prok.13.nni  nt_prok.17.nsq
    nt_prok.00.nog  nt_prok.05.nhr  nt_prok.09.nnd  nt_prok.13.nog  nt_prok.18.nhr
    nt_prok.00.nsq  nt_prok.05.nin  nt_prok.09.nni  nt_prok.13.nsq  nt_prok.18.nin
    nt_prok.01.nhr  nt_prok.05.nnd  nt_prok.09.nog  nt_prok.14.nhr  nt_prok.18.nnd
    nt_prok.01.nin  nt_prok.05.nni  nt_prok.09.nsq  nt_prok.14.nin  nt_prok.18.nni
    nt_prok.01.nnd  nt_prok.05.nog  nt_prok.10.nhr  nt_prok.14.nnd  nt_prok.18.nog
    nt_prok.01.nni  nt_prok.05.nsq  nt_prok.10.nin  nt_prok.14.nni  nt_prok.18.nsq
    nt_prok.01.nog  nt_prok.06.nhr  nt_prok.10.nnd  nt_prok.14.nog  nt_prok.19.nhr
    nt_prok.01.nsq  nt_prok.06.nin  nt_prok.10.nni  nt_prok.14.nsq  nt_prok.19.nin
    nt_prok.02.nhr  nt_prok.06.nnd  nt_prok.10.nog  nt_prok.15.nhr  nt_prok.19.nnd
    nt_prok.02.nin  nt_prok.06.nni  nt_prok.10.nsq  nt_prok.15.nin  nt_prok.19.nni
    nt_prok.02.nnd  nt_prok.06.nog  nt_prok.11.nhr  nt_prok.15.nnd  nt_prok.19.nog
    nt_prok.02.nni  nt_prok.06.nsq  nt_prok.11.nin  nt_prok.15.nni  nt_prok.19.nsq
    nt_prok.02.nog  nt_prok.07.nhr  nt_prok.11.nnd  nt_prok.15.nog  nt_prok.20.nhr
    nt_prok.02.nsq  nt_prok.07.nin  nt_prok.11.nni  nt_prok.15.nsq  nt_prok.20.nin
    nt_prok.03.nhr  nt_prok.07.nnd  nt_prok.11.nog  nt_prok.16.nhr  nt_prok.20.nnd
    nt_prok.03.nin  nt_prok.07.nni  nt_prok.11.nsq  nt_prok.16.nin  nt_prok.20.nni
    nt_prok.03.nnd  nt_prok.07.nog  nt_prok.12.nhr  nt_prok.16.nnd  nt_prok.20.nog
    nt_prok.03.nni  nt_prok.07.nsq  nt_prok.12.nin  nt_prok.16.nni  nt_prok.20.nsq
    nt_prok.03.nog  nt_prok.08.nhr  nt_prok.12.nnd  nt_prok.16.nog  taxdb.btd
    nt_prok.03.nsq  nt_prok.08.nin  nt_prok.12.nni  nt_prok.16.nsq  taxdb.bti
    nt_prok.04.nhr  nt_prok.08.nnd  nt_prok.12.nog  nt_prok.17.nhr  taxdb.tar
    nt_prok.04.nin  nt_prok.08.nni  nt_prok.12.nsq  nt_prok.17.nin  taxonomy4blast.sqlite3
</code></pre>
<pre><code>$ less -S ~/.bashrc

    export PATH=<span class="math-container">$PATH:/staging/tsailab/Blast/ncbi-blast-2.15.0+/bin
export BLASTDB=/tmp/ramdisk
export PATH=$</span>PATH:/tmp/ramdisk
    export PATH=$PATH:/tmp/ramdisk_prok
    export BLASTDB=/tmp/ramdisk_prok
</code></pre>
<pre><code>$ blastdbcmd -info -db /tmp/ramdisk_prok/nt_prok

    BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/tsailab:/tmp/ramdisk_prok:]
</code></pre>
<pre><code>$ blastn -query /staging/Blast/Input/HBV/Sample1.seq.fasta -db /tmp/ramdisk_prok/nt_prok -task blastn -evalue 1e-6 -max_hsps 1 -max_target_seqs 500 -outfmt &quot;6 qseqid qlen qstart qend sseqid slen sstart send length nident pident mismatch gaps gapopen qcovs evalue bitscore stitle sskingdoms staxids sscinames sblastnames qseq sseq&quot; -num_threads 10 -out /staging/Blast/Output/HBV/Sample1.original.txt*


    BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/Tina:/tmp/ramdisk_prok:]
</code></pre>

CC BY-SA 4.0
2024-06-01T13:28:47.733Z
First off, why are you doing this in `/tmp`? Anything in `/tmp` will be deleted when the machine reboots. Next, are your DB files in `/tmp/ramdisk_prok` or in `/tmp/ramdisk_prok/nt_prok`? You seem to show that they're in `/tmp/ramdisk_prok` but then you give blast `-db /tmp/ramdisk_prok/nt_prok`, which is it?
terdon
<database><blast>
BLAST Database error: No alias or index file found for nucleotide database
# BLAST Database error: No alias or index file found for nucleotide database

(Asked by: username_0 on 2024-05-31)

I have created a database and added environment variables, but an "error message" still appears. How can I solve it?
error message: BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/Tina:/tmp/ramdisk_prok:]

Blast Database
$ cd /tmp/ramdisk_prok

    nt_prok.00.nhr  nt_prok.04.nnd  nt_prok.08.nog  nt_prok.13.nhr  nt_prok.17.nnd
    nt_prok.00.nin  nt_prok.04.nni  nt_prok.08.nsq  nt_prok.13.nin  nt_prok.17.nni
    nt_prok.00.nnd  nt_prok.04.nog  nt_prok.09.nhr  nt_prok.13.nnd  nt_prok.17.nog
    nt_prok.00.nni  nt_prok.04.nsq  nt_prok.09.nin  nt_prok.13.nni  nt_prok.17.nsq
    nt_prok.00.nog  nt_prok.05.nhr  nt_prok.09.nnd  nt_prok.13.nog  nt_prok.18.nhr
    nt_prok.00.nsq  nt_prok.05.nin  nt_prok.09.nni  nt_prok.13.nsq  nt_prok.18.nin
    nt_prok.01.nhr  nt_prok.05.nnd  nt_prok.09.nog  nt_prok.14.nhr  nt_prok.18.nnd
    nt_prok.01.nin  nt_prok.05.nni  nt_prok.09.nsq  nt_prok.14.nin  nt_prok.18.nni
    nt_prok.01.nnd  nt_prok.05.nog  nt_prok.10.nhr  nt_prok.14.nnd  nt_prok.18.nog
    nt_prok.01.nni  nt_prok.05.nsq  nt_prok.10.nin  nt_prok.14.nni  nt_prok.18.nsq
    nt_prok.01.nog  nt_prok.06.nhr  nt_prok.10.nnd  nt_prok.14.nog  nt_prok.19.nhr
    nt_prok.01.nsq  nt_prok.06.nin  nt_prok.10.nni  nt_prok.14.nsq  nt_prok.19.nin
    nt_prok.02.nhr  nt_prok.06.nnd  nt_prok.10.nog  nt_prok.15.nhr  nt_prok.19.nnd
    nt_prok.02.nin  nt_prok.06.nni  nt_prok.10.nsq  nt_prok.15.nin  nt_prok.19.nni
    nt_prok.02.nnd  nt_prok.06.nog  nt_prok.11.nhr  nt_prok.15.nnd  nt_prok.19.nog
    nt_prok.02.nni  nt_prok.06.nsq  nt_prok.11.nin  nt_prok.15.nni  nt_prok.19.nsq
    nt_prok.02.nog  nt_prok.07.nhr  nt_prok.11.nnd  nt_prok.15.nog  nt_prok.20.nhr
    nt_prok.02.nsq  nt_prok.07.nin  nt_prok.11.nni  nt_prok.15.nsq  nt_prok.20.nin
    nt_prok.03.nhr  nt_prok.07.nnd  nt_prok.11.nog  nt_prok.16.nhr  nt_prok.20.nnd
    nt_prok.03.nin  nt_prok.07.nni  nt_prok.11.nsq  nt_prok.16.nin  nt_prok.20.nni
    nt_prok.03.nnd  nt_prok.07.nog  nt_prok.12.nhr  nt_prok.16.nnd  nt_prok.20.nog
    nt_prok.03.nni  nt_prok.07.nsq  nt_prok.12.nin  nt_prok.16.nni  nt_prok.20.nsq
    nt_prok.03.nog  nt_prok.08.nhr  nt_prok.12.nnd  nt_prok.16.nog  taxdb.btd
    nt_prok.03.nsq  nt_prok.08.nin  nt_prok.12.nni  nt_prok.16.nsq  taxdb.bti
    nt_prok.04.nhr  nt_prok.08.nnd  nt_prok.12.nog  nt_prok.17.nhr  taxdb.tar
    nt_prok.04.nin  nt_prok.08.nni  nt_prok.12.nsq  nt_prok.17.nin  taxonomy4blast.sqlite3

$ less -S ~/.bashrc

    export PATH=$PATH:/staging/tsailab/Blast/ncbi-blast-2.15.0+/bin
export BLASTDB=/tmp/ramdisk
export PATH=$PATH:/tmp/ramdisk
    export PATH=$PATH:/tmp/ramdisk_prok
    export BLASTDB=/tmp/ramdisk_prok

$ blastdbcmd -info -db /tmp/ramdisk_prok/nt_prok

    BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/tsailab:/tmp/ramdisk_prok:]

$ blastn -query /staging/Blast/Input/HBV/Sample1.seq.fasta -db /tmp/ramdisk_prok/nt_prok -task blastn -evalue 1e-6 -max_hsps 1 -max_target_seqs 500 -outfmt "6 qseqid qlen qstart qend sseqid slen sstart send length nident pident mismatch gaps gapopen qcovs evalue bitscore stitle sskingdoms staxids sscinames sblastnames qseq sseq" -num_threads 10 -out /staging/Blast/Output/HBV/Sample1.original.txt*


    BLAST Database error: No alias or index file found for nucleotide database [/tmp/ramdisk_prok/nt_prok] in search path [/home/Tina:/tmp/ramdisk_prok:]

**Tags:** database, blast
> **Comments:**
> **username_1**: First off, why are you doing this in `/tmp`? Anything in `/tmp` will be deleted when the machine reboots. Next, are your DB files in `/tmp/ramdisk_prok` or in `/tmp/ramdisk_prok/nt_prok`? You seem to show that they're in `/tmp/ramdisk_prok` but then you give blast `-db /tmp/ramdisk_prok/nt_prok`, which is it?  

---

## 1 answers

### Answer by username_2 on 2024-06-01. Score: -1

The easiest solution is to install miniconda and then install via mamba
mamba create --name myenvname blast
mamba activate blast
mamba install blast
mamba update blast
blastn -query /staging/Blast/Input/HBV/Sample1.seq.fasta -db /tmp/ramdisk_prok/nt_prok -task blastn -evalue 1e-6 -max_hsps 1 -max_target_seqs 500 -outfmt "6 qseqid qlen qstart qend sseqid slen sstart send length nident pident mismatch gaps gapopen qcovs evalue bitscore stitle sskingdoms staxids sscinames sblastnames qseq sseq" -num_threads 10 -out /staging/Blast/Output/HBV/Sample1.original.txt
mamba deactivate

Check
Do you have io permission for
/staging/Blast/Input/HBV/Sample1.seq.fasta
/staging/Blast/Output/HBV/Sample1.original.txt


To install mamba you'll need Anaconda because its within the Anaconda collection and simplifies everything on three counts, viz:

in answer to your question all configurations are automated
it is easy to automate all updates
it offers a virtual environment where code can't mess with your system
whenever you want to download other packages its the same approach

Thus all you have to do is download and install Anaconda or miniconda. From this point everything is done using conda, either:
Anaconda installs in two different locations depending on whether you install the GUI version, which makes maintenance and environments a bit easier. In the later case I think its /opt, otherwise the commandline version is ~/anadonda3.
Thereon,
conda config --add channels conda-forge
conda update -n base --all
conda install -n base mamba


---

