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Old 02-14-2010, 08:43 AM   #1
aldrinyim
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Default BWA index error

Dear all,

I never met this problem before not until I used a multiple fasta file (around 30) with each fasta sequence around 2000 to 3000 bp, is it not applicable to use short reads to map to fasta sequence of such kind?

the problem is

[bwa_index] Pack FASTA... 0.00 sec
[bwa_index] Reverse the packed sequence... 0.00 sec
[bwa_index] Construct BWT for the packed sequence...
[BWTIncConstructFromPacked] 10 iterations done. 18660 characters processed.
[BWTIncConstructFromPacked] 20 iterations done. 28804 characters processed.
[BWTIncConstructFromPacked] 30 iterations done. 32948 characters processed.
BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!

Would anyone help?
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Old 02-14-2010, 08:52 AM   #2
aldrinyim
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Oh hi everyone I just test the multiple fasta file and found that if we want an effective indexing of the fasta file, at least each fasta sequence should be >110000bp.

The program now works, thanks everyone.
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Old 02-14-2010, 09:09 AM   #3
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Quote:
Originally Posted by aldrinyim View Post
Oh hi everyone I just test the multiple fasta file and found that if we want an effective indexing of the fasta file, at least each fasta sequence should be >110000bp.

The program now works, thanks everyone.
There are two algorithms to create indexes, one for short genomes/references, and one for long genomes/references. The default is the algorithm for long references so you have to specify "-a is" to run the algorithm for the short reference.
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Old 02-14-2010, 10:03 AM   #4
aldrinyim
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Thanks nilshomer for reminding me of that, because i wrote a few scripts for BWA, I mistakenly used the script using dbwtsw for the short genome.

The problem should be fixed now!
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