HW2 - Introduction to Biocluster and Linux

2 minute read

Topic: Linux Basics

1. Log into your user account on the HPCC cluster, and from there into a compute node with srun. Note, the following code is also available in pure text format here. The following command may return a DISPLAY error if X11 is not enabled in a session. If this happens, drop the argument --x11in the below command. Users logging in from a macOS computer, need to have XQuartz installed for X11 support (see here).

   srun --x11 --partition=short --mem=2gb --cpus-per-task 4 --ntasks 1 --time 1:00:00 --pty bash -l
   

2. Download code from this page

   wget https://cluster.hpcc.ucr.edu/~tgirke/Linux.sh --no-check-certificate 
   

3. Download Halobacterium proteome and inspect it

   wget https://ftp.ncbi.nlm.nih.gov/genomes/genbank/archaea/Halobacterium_salinarum/all_assembly_versions/GCA_004799605.1_ASM479960v1/GCA_004799605.1_ASM479960v1_protein.faa.gz
   gunzip GCA_004799605.1_ASM479960v1_protein.faa.gz
   mv GCA_004799605.1_ASM479960v1_protein.faa halobacterium.faa
   less halobacterium.faa # press q to quit
   

4. How many protein sequences are stored in the downloaded file?

   grep '>' halobacterium.faa | wc
   grep '^>' halobacterium.faa --count
   

5. How many proteins contain the pattern WxHxxH or WxHxxHH?

   egrep 'W.H..H{1,2}' halobacterium.faa --count
   

6. Use less to find IDs for pattern matches or use awk

   awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | less
   awk --posix -v RS='>' '/W.H..(H){1,2}/ { print ">" $0;}' halobacterium.faa | grep '^>' | cut -c 2- | cut -f 1 -d\ > myIDs
   

7. Create a BLASTable database with formatdb

   module load ncbi-blast/2.2.31+
   makeblastdb -in halobacterium.faa -out halobacterium.faa -dbtype prot -hash_index -parse_seqids
   

8. Query BLASTable database by IDs stored in a file (e.g. myIDs)

   blastdbcmd -db halobacterium.faa -dbtype prot -entry_batch myIDs -get_dups -out myseq.fasta
   

9. Run BLAST search for sequences stored in myseq.fasta

   blastp -query myseq.fasta -db halobacterium.faa -outfmt 0 -evalue 1e-6 -out blastp.out
   blastp -query myseq.fasta -db halobacterium.faa -outfmt 6 -evalue 1e-6 -out blastp.tab
   

10. Return system time and host name

    date
    hostname
    

Additional exercise material in Linux Manual

Homework assignment

Perform above analysis on the protein sequences from E. coli. A right click on the link will allow you to copy the URL so that it can be used together with wget. Record result from final BLAST command (with outfmt 6) in text file named myresult.txt.

Homework submission

Upload result file (myresult.txt) to your private course GitHub repository under Homework/HW2/HW2.txt.

Due date

Most homeworks will be due one week after they are assigned. This one is due on Thu, April 10th at 6:00 PM.

Homework solution

See here.