mluypaert - 2015-03-31

Used Bowtie version: 1.1.1

I created a Bowtie index for the Ensembl 78 human genome ( from one file, containing regular chromosomes as well as haplotypes (HSCHR) as patches. This resulted in the following index files:

-rw-rw-r-- 1 root root 831M 2015-03-23 15:50 lib.1.ebwtl
-rw-rw-r-- 1 root root 719M 2015-03-23 15:50 lib.2.ebwtl
-rw-rw-r-- 1 root root 772K 2015-03-23 14:18 lib.3.ebwtl
-rw-rw-r-- 1 root root 719M 2015-03-23 14:18 lib.4.ebwtl
-rw-rw-r-- 1 root root 831M 2015-03-23 17:25 lib.rev.1.ebwtl
-rw-rw-r-- 1 root root 719M 2015-03-23 17:25 lib.rev.2.ebwtl

However when I try to run bowtie using this index, I get the following error:

Could not locate a Bowtie index corresponding to basename "large_idx/lib"

I am 99.99% sure that the provided directory is the correct location of the index.

For debugging purpose, I tried to create both a small and a large index starting from the same (small) fasta-file (using the '--large-index' option for creating the large index).

These files are in the small index:

total 8.1M
-rw-rw-r-- 1 root root 4.1M 2015-03-31 13:32 lib.1.ebwt
-rw-rw-r-- 1 root root 8 2015-03-31 13:32 lib.2.ebwt
-rw-rw-r-- 1 root root 26 2015-03-31 13:32 lib.3.ebwt
-rw-rw-r-- 1 root root 5 2015-03-31 13:32 lib.4.ebwt
-rw-rw-r-- 1 root root 4.1M 2015-03-31 13:32 lib.rev.1.ebwt
-rw-rw-r-- 1 root root 8 2015-03-31 13:32 lib.rev.2.ebwt

And these files are in the large index:

total 17M
-rw-rw-r-- 1 root root 8.1M 2015-03-31 13:28 lib.1.ebwtl
-rw-rw-r-- 1 root root 12 2015-03-31 13:28 lib.2.ebwtl
-rw-rw-r-- 1 root root 46 2015-03-31 13:28 lib.3.ebwtl
-rw-rw-r-- 1 root root 5 2015-03-31 13:28 lib.4.ebwtl
-rw-rw-r-- 1 root root 8.1M 2015-03-31 13:28 lib.rev.1.ebwtl
-rw-rw-r-- 1 root root 12 2015-03-31 13:28 lib.rev.2.ebwtl

Running bowtie on the small index succeeded, using the large index failed again with the same error message describe above.

Am I missing something here or is bowtie 1.1.1 unable to run using a large index?

 

Last edit: mluypaert 2015-03-31