Fatal Limit Error: Star RNA Sequencing

When you issue the RNA sequencing GenPipes pipeline with Star option commands, the jobs fails with the fatal limit error:

Fatal LIMIT error: the number of junctions to be inserted on the fly =2663181 is larger than the limitSjdbInsertNsj=1000000
Fatal LIMIT error: the number of junctions to be inserted on the fly =2663181 is larger than the limitSjdbInsertNsj=1000000
SOLUTION: re-run with at least --limitSjdbInsertNsj 2663181

Nov 29 14:10:58 ...... FATAL ERROR, exiting
MUGQICexitStatus:104

It is not clear from the error message where this solution configuration option needs to be specified.

Typically, the Star index options in the `.ini` file supplied for RNA sequencing protocol do not show `--limitSjdbInsertNsj` option.

[star_index]

ram = 191000M
io_buffer = 1G
threads = 20
cluster_cpu = -N 1 -c 40
cluster_walltime = --time=15:00:0
cluster_queue = --mem-per-cpu=4775M
star_cycle_number = 99

Fix

The correct way to specify this option is using `--other-option` flag as shown in the snippet from `.ini` file below:

[star_index]

ram = 191000M
io_buffer = 1G
threads = 20
cluster_cpu = -N 1 -c 40
cluster_walltime = --time=15:00:0
cluster_queue = --mem-per-cpu=4775M
star_cycle_number = 99
other_options =--limitSjdbInsertNsj  2500000