Hi, I'm trying to align my reads to a reference genome (HG38) using the bwa alignment. I used this command: bwa aln -o 2 -n 11 -k 7 -N -l 11 -m 1000000000 genome.fa ANNCNNGGAGTATATCAAAAGAATAAGG.fa > aln_out.sa
Which gives me an error saying “[bwa_aln_core] calculate SA coordinate... Killed” even though I am running this command on a Unix system with 32GB RAM and 100 GB space. I guess it is not due to limited resources on the system i am running it on. This command is run for NNGRRT PAM (SpCas9). However, running the same command for queue size (m parameter) 10^7 instead of 10^9 works fine. It would be a great help if you can help me understand why this is happening?. And also if you can help me understand the queue size parameter better. Read sequence used is the sequence mentioned in the command.
Thank you.
