Bowtie cannot find genomes in directory

[huzefa_mehta]

I am running bowtie (1) and the tool doesnt seem to recognize the indexes (although they are present in the directory, I have specified). Any clues?

ubuntu@ip-172-31-15-51:~$ ./rung
Could not locate a Bowtie index corresponding to basename "/home/ubuntu/bowtie-indexes/mm9"
Command: /home/ubuntu/bowtie-master/bowtie-master/bowtie -m 1 -p 6 -S /home/ubuntu/bowtie-indexes/mm9 fastq/myc.fastq.gz myc.sam
ubuntu@ip-172-31-15-51:~$ ls bowtie-indexes/mm9
chr10.fa chr13.fa chr16.fa chr19.fa chr3.fa chr6.fa chr9.fa chrY.fa mm9.2.ebwt mm9.ebwt.zip mm9.rev.2.ebwt
chr11.fa chr14.fa chr17.fa chr1.fa chr4.fa chr7.fa chrM.fa make_mm9.sh mm9.3.ebwt mm9.fa
chr12.fa chr15.fa chr18.fa chr2.fa chr5.fa chr8.fa chrX.fa mm9.1.ebwt mm9.4.ebwt mm9.rev.1.ebwt

[mastal]

I think you have to give the basename of the index, as well as the directory,
so in your case that would be:
"/home/ubuntu/bowtie-indexes/mm9/mm9"

[bishwo]

merge all chr file to one and create bowtie index of that files or create bowtie index from single whole genome file. It seems bowtie does not take indices of separate chromosome files.

I have following bowtie index which works fine

[use@localhost Desktop]$ ls /home/references/iGenomes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex/
genome.1.ebwt genome.2.ebwt genome.3.ebwt genome.4.ebwt genome.fa genome.rev.1.ebwt genome.rev.2.ebwt

P.S. like @mastal said give base name (without extension). In my case bowtie index is /home/references/iGenomes/Mus_musculus/UCSC/mm10/Sequence/BowtieIndex/genome and single whole genome file is genome.fa

[tokitky]

It is too late to answer this thread, but for the people who will face similar problems.

I've just had similar problems when I run the bowtie with ubuntu on Acer netbook (4GB memory).

The error message said as follows;

could not locate a bowtie index corresponding to basename "mm9"

At that time, I did not have enough space on my hard drive since there were several fastq files on my netbook, and the system seemed not to be stable.

I remove all of the fastq files other than the one which is using for bowtie, then tried to start bowtie. Since then, I had never seen the error message.