Blast++/Example

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As an example for a blast++ job, we are doing a simple query of the sequence test.fasta

[leonhard@euler06 ~]$ cat test.fasta 
>sequence1
MIKKIGVLTSGGDAPGMNAAIRGVVRSALTEGLEVMGIYDGYLGLYEDRMVQLDRYSVSD
MINRGGTFLGSARFPEFRDENIRAVAIENLKKRGIDALVVIGGDGSYMGAMRLTEMGFPC
IGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLA
AAIAGGCEFVVVPEVEFSREDLVNEIKAGIAKGKKHAIVAITEHMCDVDELAHFIEKETG
RETRATVLGHIQRGGSPVPYDRILASRMGAYAIDLLLAGYGGRCVGIQNEQLVHHDIIDA
IENMKRPFKGDWLDCAKKLY

and compare it against the nt database.

[leonhard@euler06 ~]$ module load gcc/4.8.2 blast/2.2.30
[leonhard@euler06 ~]$ bsub -n 1 -W 4:00 -R "rusage[mem=2048]" "blastp -query test.fasta -out output.blast.txt -db nr"
Generic job.
Job <33641518> is submitted to queue <normal.4h>.
[leonhard@euler06 ~]$ bjobs
JOBID      USER      STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33641518   leonhard  PEND  normal.4h  euler06
[leonhard@euler06 ~]$ bjobs
JOBID      USER      STAT  QUEUE      FROM_HOST   EXEC_HOST   JOB_NAME   SUBMIT_TIME
33641518   leonhard  RUN   normal.4h  euler06     e1057       *xt -db nr Dec  6 10:02
[leonhard@euler06 ~]$ bjobs
No unfinished job found

The result is then written to the output file output.blast.txt:

[leonhard@euler06 ~]$ sed -n '25,40p' output.blast.txt 
Query= sequence1

Length=320
                                                                     Score     E
Sequences producing significant alignments:                          (Bits)  Value

ref|WP_000591795.1|  MULTISPECIES: ATP-dependent 6-phosphofructok...    650   0.0   
gb|EFJ85506.1|  6-phosphofructokinase [Escherichia coli MS 84-1]        651   0.0   
gb|ABF05609.1|  6-phosphofructokinase I [Shigella flexneri 5 str....    651   0.0   
ref|WP_024228092.1|  ATP-dependent 6-phosphofructokinase [Escheri...    650   0.0   
gb|ABE09911.1|  6-phosphofructokinase isozyme I [Escherichia coli...    651   0.0   
gb|ADX52955.1|  6-phosphofructokinase [Escherichia coli KO11FL]         651   0.0   
ref|WP_000967668.1|  ATP-dependent 6-phosphofructokinase [Escheri...    651   0.0   
ref|WP_032279226.1|  MULTISPECIES: ATP-dependent 6-phosphofructok...    649   0.0   
gb|EEJ48186.1|  6-phosphofructokinase [Escherichia coli 83972]          650   0.0   
ref|WP_039061908.1|  MULTISPECIES: ATP-dependent 6-phosphofructok...    649   0.0   

You can find the resource usage summary of the job in the corresponding LSF log file.