Bowtie-build index file generation, no *.3.ebwt, *.4.ebwt

[Bardj]

Hi all,
I am working on aligning a set of paired-end reads with bowtie. I am trying to generate my reference index using:

/data/apps/bowtie/./bowtie-build -r pombe_fasta/chromosome1.fasta,pombe_fasta/chromosome2.fasta,pombe_fasta/chromosome3.fasta pombe_indexes/

It generates pombe.1.ebwt, pombe.2.ebwt,pombe.1.rev.ebwt,pombe.2.rev.ebwt

When that failed to generate the files for paired-end alignment i tried the -3 option which also didn't generate the files.

I was wondering what I can do to generate the two files needed for paired-end alignments, or if anyone has pre-built indexs for Pombe.

I am utilizing:
/data/apps/bowtie/bowtie-build version 0.11.3
64-bit
Built on privet.umiacs.umd.edu
Mon Oct 12 18:08:44 EDT 2009
Compiler: gcc version 3.4.6 20060404 (Red Hat 3.4.6-10)
Options: -O3 -m64
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

[Ben Langmead]

The -r option suppresses those files. Not specifying -r should fix it.

Thanks,
Ben

[Bardj]

Thanks for the quick reply Ben.

I ran it again removing the -r option,

/data/apps/bowtie/./bowtie-build pombe_fasta/chromosome1.fasta,pombe_fasta/chromosome2.fasta,pombe_fasta/chromosome3.fasta pombe_indexes/

And the files still aren't being generated. I tried just having the -3 option, and this is the output:

/data/apps/bowtie/./bowtie-build -3 pombe_fasta/chromosome1.fasta,pombe_fasta/chromosome2.fasta,pombe_fasta/chromosome3.fasta pombe_indexes/
Settings:
Output files: "pombe_indexes/.*.ebwt"
Line rate: 6 (line is 64 bytes)
Lines per side: 1 (side is 64 bytes)
Offset rate: 5 (one in 32)
FTable chars: 10
Strings: unpacked
Max bucket size: default
Max bucket size, sqrt multiplier: default
Max bucket size, len divisor: 4
Difference-cover sample period: 1024
Reference base cutoff: none
Endianness: little
Actual local endianness: little
Sanity checking: disabled
Assertions: disabled
Random seed: 0
Sizeofs: void*:8, int:4, long:8, size_t:8
Input files DNA, FASTA:
pombe_fasta/chromosome1.fasta
pombe_fasta/chromosome2.fasta
pombe_fasta/chromosome3.fasta
Reading reference sizes
Time reading reference sizes: 00:00:01
Total time for call to driver() for forward index: 00:00:01
Reading reference sizes
Time reading reference sizes: 00:00:00
Total time for backward call to driver() for mirror index: 00:00:00

[Ben Langmead]

The basename you specified ("pombe_indexes/") will result in the files being named pombe_indexes/.3.ebwt and pombe_indexes/.4.ebwt. They're probably there, it's just that you won't see them unless you do "ls -a" to list files that start with ".". You probably want to use a basename more like "pombe_indexes/pombe".

Hope that helps,
Ben

[Bardj]

Ah thanks very much, a big oversight on my part. The files were indeed there, and changing the base name worked. Thanks very much for the help, I feel rather silly for overlooking that detail!