I have tried to index 34GB worth of primate genomes in one single go using
bwa -a bwtsw and it went all the way into doing that but then crashed at this point:
[BWTIncConstructFromPacked] 7090 iterations done. 70465272750 characters processed. [BWTIncConstructFromPacked] 7100 iterations done. 70493213214 characters processed. [BWTIncConstructFromPacked] 7110 iterations done. 70518042750 characters processed. [bwa_index] 118525.77 seconds elapse. [bwa_index] Update BWT... /tools/lsf/spool/1327577148.2686228: line 8: 7412 Segmentation fault (core dumped) ~/src/bwa/bwa-0.6.1/bwa index -a bwtsw primates.fa
I tried this on a 30000M job, trying again now (still chugging along) on 60000M.
Any suggestions on what might be happening here?