View Single Post
Old 11-13-2011, 08:18 PM   #20
alig
Member
 
Location: adelaide

Join Date: Sep 2008
Posts: 43
Default Bfast Malloc memory error

Hi,
Has there been a solution to the Malloc memory error when running Bfast?

I am having the same problem when trying to run bfast bwaaln

bfast+bwa-0.7.0a/bfast/bfast bwaaln -n 0.04 -o 1 -e -1 -d 5 -i 5 -l 25 -k 2 -M 3 -t 8 -O 11 -E 4 -c -q 20 bfast_bwa_index/hg18_noran_mask.fa T3460_R3.fastq > bfast_matches_R3_bwa_T3460.bmf
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_read_seq] 2.0% bases are trimmed.
[bwa_aln_core] calculate SA coordinate... 138.80 sec
[bwa_aln_core] write to the disk... ************************************************************
In function "bwa_aln_core": Fatal Error[MallocMemory]. Message: Could not allocate (malloc) memory.
***** Exiting due to errors *****

I am running on Ubuntu with 32 Gb RAM.

Any help would be greatly appreciated

thanks alig
alig is offline   Reply With Quote