I'm trying to align my reads to a reference genome and I got this error (using the attached line). Reading previous comments I've seen that the last Bowtie version (2.3.4) should fix this problem. However, I'm using this version and I got the same error. I've also read it has something to do with memory...here my free-g screenshot. Can you help me, please? I'm quite new at that...so I don't know what's going on!
$ bowtie2 --local --trim5 11 -x mm9 -U read1.barcoded.fastq.gz -S example.sam
version: Bowtie 2 version 220.127.116.11 by Ben Langmead ...
Thanks in advance!