Error while running All-against-All alignments in OMA

Question

[pragyadeeproy]

hello, i am trying to use OMA standalone on an SGE using only 2 transcriptomes (centipedes, transcript assemblies). However the all-against-all alignment step is crashing everytime with this error : "ERROR: job_idx not an integer: undefined". I use qsub to submit the jobs. Could anyone suggest me where I am going wrong, or an alternative? My job submission script is as follows:

#!/bin/bash

#$ -N run_oma_part2
#$ -l h_vmem=256G
#$ -pe smp 16
#$ -cwd
#$ -o ./logs/part2.output

export NR_PROCESSES=16 ../bin/oma -s -W 7000

[LauferVA]

the error is not with all-against-all alignment. the error is in the initial step - in which you try to qsub the job...

Answer 1

[Adrian Altenhoff]

Hi @pragyadeeproy

you need to start the oma computations as job-arrays, not with shared memory parallelization. The individual jobs don't need to communicate, so job arrays are much more efficient as you can also start them on different compute nodes.

#!/bin/bash

#$ -N run_oma_part2
#$ -l h_vmem=20G 
#$ -t 1-100
#$ -cwd
#$ -o ./logs/part2.output

export NR_PROCESSES=100
../bin/oma -s -W 7000

Best wishes Adrian