maximum number of the reference input files for bowtie-build

[joseph]

Hi
Is there a maximum number of the reference input files for bowtie-build?
I am trying to build a Bowtie index from a set of 500 DNA sequences; I get the following error:

Error: could not open seq_x.fa

When I remove seq_x.fa and all the seq_*.fa after it, bowtie-build works fine.
What do you do when you have a high number of reference input files?
I am using Bowtie 0.12.5.

[john_mu]

using "seq_*.fa" won't work with bowtie-build, the output won't be all your sequence files.

If you want to input a list you need to separate each file with commas.

I'm not sure why it fails with your FASTA file, you'll have to wait for Ben Langmead to reply.

[joseph]

using "seq_*.fa" won't work with bowtie-build, the output won't be all your sequence files.

If you want to input a list you need to separate each file with commas.

I'm not sure why it fails with your FASTA file, you'll have to wait for Ben Langmead to reply.

I used files separated with commas:

bowtie-build -f seq1.fa,seq2.fa,...,seqn.fa my_ebwt_base