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Old 07-21-2015, 11:08 PM   #1
Junior Member
Location: Manipal

Join Date: Jul 2013
Posts: 6
Default Bowtie large index error

This is a duplicate from biostar. I have not found a solution to it. I build large index using bowtie "bowtie-build --large-index" for a multi fasta genome of approx 10 GB.
Index is created successfully, but when i run bowtie with the fastq file it says.

bowtie index -q ../reads.fastq
Could not locate a Bowtie index corresponding to basename "index"
Command: bowtie --wrapper basic-0 -q index ../reads.fastq

My indexes have the extension .ebwtl. I have tried giving absolute paths for the index and dataa file. As well as running the command from the index folder.

Also, tried the same using bowtie 1.1.1 and 1.1.2 to build the index and analyse.

Any suggestions?

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Old 07-22-2015, 03:21 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You'll likely need to modify the bowtie perl script, since this appears to be a bug. You should also report this bug to the developers.
dpryan is offline   Reply With Quote

.ebwtl, bowtie, large index

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