Skip to content

Blast on BiBiGrid tutorial

Database Repositories

The Bielefeld de.NBI Cloud hosts a public bucket called biodata which mirrors some databases from public repositories. To check out which databases are available, list the bucket using your favorite command line client.

Download Linux version of minio:

cd ~
chmod +x mc

~/mc config host add s3-bi <YOUR-ACCESS-KEY> <YOUR-SECRET-KEY>

The following command will list all BLAST databases in the ''biodata'' bucket:

~/mc ls s3-bi/biodata/blast/
[2018-03-07 13:42:34 UTC] 118MiB swissprot.00.phr
[2018-03-07 13:42:30 UTC] 3.6MiB
[2018-03-07 13:42:31 UTC] 4.2MiB swissprot.00.pnd
[2018-03-07 13:42:31 UTC]  17KiB swissprot.00.pni
[2018-03-07 13:42:30 UTC] 1.8MiB swissprot.00.pog
[2018-03-07 13:42:30 UTC] 3.6MiB swissprot.00.ppd
[2018-03-07 13:42:30 UTC]  14KiB swissprot.00.ppi
[2018-03-07 13:42:31 UTC]  25MiB swissprot.00.psd
[2018-03-07 13:42:30 UTC] 603KiB swissprot.00.psi
[2018-03-07 13:42:36 UTC] 169MiB swissprot.00.psq
[2018-03-07 13:42:30 UTC]    31B swissprot.pal

For this tutorial we will use the SwissProt database to run some BLAST searches on the BiBiGrid cluster.

Query Sequences: toy data set

A toy data set is available at here:

cd /vol/spool

BLAST installation

Our BiBiGrid cluster does not have any special software installed. Usually, you would configure your VMs while setting up the BiBiGrid cluster, or you could use Docker to pull the software you need. We are just going to install BLAST on each node via ''apt'' (in this case, we have 4 nodes with 2 cores each):

qsub -cwd -pe multislot 2 -t 1-4 -b y /usr/bin/sudo apt install --yes ncbi-blast+

BLAST database download

After setting up an s3 client (minio in this case), we can download the BLAST database ''swissprot'' from SWIFT to the cluster-wide shared directory ''/vol/spool'':

cd /vol/spool
~/mc cp --recursive s3-bi/biodata/blast/ .

Run the BLAST jobs BLAST database download

pip install numpy
pip install pyfasta
pyfasta split -n 10 mystery.faa

Submit your jobs to the SGE:

for i in *.[0-9][0-9].faa
qsub -cwd -b y /usr/bin/blastp -db swissprot -query $i -out $i.blast.out

You can check the cluster load at ''http://BIBIGRID_MASTER/ganglia''