Computational Quantitative Life Science cluster at Oregon State University

CQLS@OSU

Setup and setting of the Computational Quantitative Life Science cluster

You've been given an account on the following machine:

           shell.cgrb.oregonstate.edu

           Command Line Access:
           ssh -p X username@shell.cgrb.oregonstate.edu
           
           This is to avoid get disconnected often
           ssh -X -o ServerAliveInterval=30 -p X username@shell.cgrb.oregonstate.edu
     
           Please use the following machine to upload and download data:
           Server:

           	files.cgrb.oregonstate.edu

           SFTP Access:
           	sftp -o Port=X username@files.cgrb.oregonstate.edu
           	scp -P X <files to upload> username@files.cgrb.oregonstate.edu:
           
           Samba/SMB Access:
           	Windows: \\files.cgrb.oregonstate.edu
           	Mac: smb://files.cgrb.oregonstate.edu

Notes: All programs are in /local/cluster/ Aparently, you have to call each program from its PATH, so double check that carefully. Also, the nodes are specified independently, so double-check that you are running optimally.

Activating conda: CQLS qsub

eval "$(conda shell.bash hook)"
conda activate <package>

Setting up GitHub

Follow this instructions: https://github.com/ricardoi/CQLS/tree/main/git

Working on the CQLS-OSU cluster

Scheduler

SGE infrastructure of the CQLS-OSU cluster SGE submission examples

# general submission work
SGE_Batch -c “./tu script” -P 1 -q bpp -r jobname
# specific hots submission work
SGE_Batch -c “./tu script” -P 1 -q bpp@cerebro -r jobname

Development session

# running development session in a specific host
qrsh -q bpp@cerebro
# requesting multiple processors
qrsh -q bpp@anduin -pe thread 16
# requesting memory
qrsh -q bpp@anduion -l mem_free=120G

Note: you can use the commands below to specify memory, processors, etc.

NCBI DATABASES @ CQLS

The database can be called from $BLASTDB

echo $BLASTDB
ls -lth $BLASTDB/ 
$/nfsi1/CGRB/BlastDB/NCBI/v5/latest_blast_DB -> blast_20220421
# execute
SGE_Batch -c 'blastn -query file.fasta -db nt -out blast_results.bl -num_threads 4' -P 4 -q bpp -r blastn

Avoid these nodes::

There are some nodes that just don't work.

qsub -q *@!(samwise*|nem*)

Anduin node got fixed.

Basic Usage: SGE_Batch -c '<command>' -m <max_memory> -f <free_mem_request> -F <max_file_size> -P <number_processors> -r <Run_ID> -p <priority> -M <email_address> -q <queue> -Q -c The command to submit. (REQUIRED: Make sure to use '')
-t Array Job Range to submit (e.g. 1-100).
-b Array Job Maximum Task Concurrency ('batch size'; default 50).
-F Kill the job if any created file exceeds this size (100M, 1G, 4G, 32G etc.).
-f Free memory to request on the machine to run this job (100M, 1G, 4G, 32G etc.).
-m Maximum memory this job may use (kill if exceeded) (100M, 1G, 4G, 32G etc.).
-P The number of processors needed for this job if you have a threaded application (default 1).
-r The SGE RunID and Log Output Directory Name. (REQUIRED)
-q The QUEUE to use. (default to use any node you have access to)
-Q Don't print any output to the screen. (Use then when you are running many jobs at once).
-p The priority of job submitted. (range -10 to 10, default 0)
-M Email address to send notification at beginning and end of job.
-S Shell option: Setting this option will change the default shell from "bash" to "tcsh". (defualt "bash").
-h Print Help Page.
-l mem_free Specify the amount of memory needed.
-l s_vmem Sepecify the soft limit of memory requested - pass ot to SIGNIN to the program.
-l h_vmem Specify the hard limit of memory request - if your job exceed this limit, it will be killed

CQLS available host

$ SGE_Avail
#                 HOST TOTRAM FREERAM    TOTSLOTS                 Q  QSLOTS  QFREESLOTS   QSTATUS     QTYPE
#                 amp  1007.6   977.5         128               bpp     107         107    normal       BIP
#             cerebro  1007.3   986.6         256               bpp     171         103    normal       BIP
#              anduin*  1007.6  977.5         128               bpp      86          86    normal       BIP
#              selway  1007.6   964.1         128               bpp      86          86    normal       BIP
#           symbiosis  1007.4   991.7         128               bpp      89          67    normal       BIP
#              debary  1007.6   936.9         128               bpp      86          50    normal       BIP
#               galls   503.7   477.0          64               bpp      44          24    normal       BIP
#               cedro   503.7   492.1          64               bpp      44          18    normal       BIP

• LeBoldus primary host, also Fangorn - not listed.

Category	State	SGE Letter Code
Pending	pending	qw
Pending	pending, user hold	qw
Pending	pending, system hold	hqw
Pending	pending, user and system hold	hqw
Pending	pending, user hold, re-queue	hRwq
Pending	pending, system hold, re-queue	hRwq
Pending	pending, user and system hold, re-queue	hRwq
Pending	pending, user hold	qw
Pending	pending, user hold	qw
Running	running	r
Running	transferring	t
Running	running, re-submit	Rr
Running	transferring, re-submit	Rt
Suspended	obsuspended	s, ts
Suspended	queue suspended	S, tS
Suspended	queue suspended by alarm	T, tT
Suspended	allsuspended withre-submit	Rs,Rts,RS, RtS, RT, RtT
Error	allpending states with error	Eqw, Ehqw, EhRqw
Deleted	all running and suspended states with deletion	dr,dt,dRr,dRt,ds, dS, dT,dRs, dRS, dRT

source

---

Creating conda environments

conda create --name NEW_ENV python=3
conda activate NEW_ENV
conda deactivate NEW_ENV
# checking list enviroment
conda env list

to modify the long path use: conda config --set env_prompt '({name})'
Cheat sheet: conda environments

To load conda environments from bash

eval "$(conda shell.bash hook)"
conda activate RepeatMakser

Subnmitting tickets to CQLS:

https://shell.cqls.oregonstate.edu/support/

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Metapipeline

Raw pipeline for PacBio genome assemblies of P. ramorum

"Assembly reads" 
   Nextdenovo -> Pacbio # reads assembly
   "QStats "
      assembly -> Braker # contig annotation
      "Genome annotated"
         <Comparative genomics> -> What Tools?

Suggested and notes

hgap-4 -> Falcon-unzip -> purge_haplotigs -> SSPACE_LongRead

#for nano pore assemblies

flye # to aassembly de novo 

---

Setting $PATH and env

in .bashrc add

export PATH=$PATH:/.local/to_folder

and in the .tcshrc, set the enviroment by adding

set PATH $HOME/.local/to_folder/:$PATH

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CGRB/CQLS useful links

CGRB infrastructure and you
CGRB infrastructure
UNIX hpc cluster basic information
Unix home - tips and more

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