Error: RNA Sequencing Star alignment - Out of Memory

For first time users, it has been observed (see example in Google GenPipes Forum) that the RNA Sequencing pipeline command execution stops after STAR alignment 1.

Fix

try to change the STAR parameters in your ini files to something like in the .ini files of the master branch:

https://bitbucket.org/mugqic/mugqic_pipelines/src/master

The problem should be solved by setting io_buffer to a higher value like 1G or 4G. The command you show indicates you are using 8M.

At some point io_buffer was decreased in the template .ini but this exposed a bug in STAR where a negative memory allocation is attempted.