Which script to use when submitting job with trinity in apocrita?

Question

[oshin707]

So I have been trying to submit a job on apocrita with use of trinity but I have been getting the script wrong. and they say the job has been submitted but i cant see the status by using qstat or anything. can anyone suggest a solution.

i have used this script.

#! /bin/sh

#$ -cwd

#$ -V

#$ -N transcriptomereads

#$ -o transcriptomereads.out

#$ -j y

#$ -l h_vmem=2G

#$ -pe smp 10

module load trinity/2.2.0

module load java/oracle/1.8.0_11

Trinity --seqType fq --single transcriptomereads.trimmed.fq.gz --CPU 10 --max_memory 20G

[GenoMax]

Is apocrita a cluster you are submitting this job to? If so it would be best to contact your local cluster admins.

BTW: Trinity needs plenty of RAM so make sure you make that available. 20G is likely not going to cut it with 10 cores.

[oshin707]

i just want to know the basic script format to submit job using trinity. how can i do that? its for an assignment.

[GenoMax]

Exact script your cluster requires is going to be dependent on job scheduler it uses and local policies. The trinity command you have in the script above looks ok as far as that format goes.

What job scheduler is your cluster using?

[oshin707]

i m like a completely new student with microbiology background and zero experience with bioinformatics. so please forgive me if i am wrong. but by job scheduler do u mean where we submit jobs via? it is Sun Grid Engine

[GenoMax]

That is correct.

If it is the same apocrita cluster as you are referring to then this link gives you help about how to submit jobs.

Trinity processes require 10G memory each so modify this parameter to

#$ -l h_vmem=10G

Also add (if not there)

#$ -M your_valid_email_address

So you get some email from the cluster about what is going on.

[oshin707]

ok thank you. i will try this.

[oshin707]

hi so it did run. but stopped becz of lack of memory. what should i do now? h_vmem and increase max_memory?

[GenoMax]

How much total memory is your account allowed to use? Divide memory number by 10 and change the number of cores to that number in the --CPU option and #$ -pe smp