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Old 03-24-2011, 12:28 AM   #1
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Location: EU

Join Date: Mar 2011
Posts: 2
Default Bowtie with many entries (>) in index

I am using bowtie to align Illumina GAII sequences to two different refrerences. One is contining large contigs and have about 20 000 entries (> in fasta file about 1.4 Gb) and the other contains over 3 million entries (> in fasta file, about 2.3 Gb). Now the problem is that when I try to align reads to the large index, it takes a long time, by that I mean several hours, much longer than it takes to align to the human genome which is bigger in terms of Gb.

I also check the CPU usage, when I run against the human genome or my smaller index, user cpu is at 100% but with the big index, system CPU is running at 12% or similar. I checked with my sys admin and he said that bowtie was waiting for a system call "read" and it looked like it was reading one byte at a time.

changing the offrate to e.g. 3 from 5 makes it worse but memory is NOT exhausted in either case (total memory is 72GB). Does anyone have similar problems? Any suggestions?
fredrik01 is offline   Reply With Quote

bowtie, index, system cpu

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