Question: Could not locate a bowtie index corresponding to basename -- tried previously posted solutions
gravatar for nichgentry
15 months ago by
nichgentry0 wrote:


I am running on Ubuntu 16 and am trying to analyze my data with Bowtie2. I have managed to get this exact script to work on a windows machine running cygwin, but can't figure out this problem that arose on Linux.

I am getting the classic "Could not located Bowtie index corresponding to basename "directory", yet I have listed a path directing to the base file name 'mm10', not the folder as many people here have posted about before.

Things that I have tried:

Changing to directory the index is located and running bowtie2.

Adding the directory the index is located in to PATH.

Placed the index in a folder in the bowtie2 directory, in my downloads directory, and the desktop. All with the same result.

I have tried building an index from scratch or downloading a prebuilt one from bowtie2.

I am running the code within a script to align multiple reads, but I have also tried manually calling bowtie to individual fastq files.

bowtie2 index:
call to bowtie2: 
bowtie2 --local --very-sensitive-local --no-unal -q --phred33 --threads 12 -x /user/home/Downloads/mm10/mm10 -U BS_P384R_S_S30_L002_R1_001.fastq > BS_P384R_S
Could not locate a Bowtie index corresponding to basename "/user/home/Downloads/mm10/mm10"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/user/anaconda3/bin/bowtie2-align-s --wrapper basic-0 --local --very-sensitive-local -q --phred33 --threads 12 -x /user/home/Downloads/mm10/mm10 --passthrough -U BS_P384R_S_S30_L002_R1_001.fastq 
(ERR): bowtie2-align exited with value 1
Traceback (most recent call last):
  File "/home/user/phd/", line 92, in <module>
    py_bowtie_single_end('/home/user/phd/NGYHF03', list_output_sam = outputs, bowtie2_index = mm10)
  File "/home/user/phd/", line 87, in py_bowtie_single_end
    check_output(temp_str, shell=True)
  File "/home/user/anaconda3/lib/python3.6/", line 336, in check_output
  File "/home/user/anaconda3/lib/python3.6/", line 418, in run
    output=stdout, stderr=stderr)
subprocess.CalledProcessError: Command 'bowtie2 --local --very-sensitive-local --no-unal -q --phred33 --threads 12 -x /user/home/Downloads/mm10/mm10 -U BS_P384R_S_S30_L002_R1_001.fastq > BS_P384R_S' returned non-zero exit status 1.

Any suggestions on something to try?

index error alignment bowtie2 • 1.2k views
ADD COMMENTlink modified 15 months ago by Vimalkumar Velayudhan190 • written 15 months ago by nichgentry0
gravatar for Vimalkumar Velayudhan
15 months ago by
Vimalkumar Velayudhan190 wrote:

Path specified in -x should be /home/user/Downloads/mm10/mm10 instead of /user/home...

ADD COMMENTlink written 15 months ago by Vimalkumar Velayudhan190

My mistake, that was a typo when I was trying to edit the script to remove extra identifying factors. The actual line reads correctly as you have described.

ADD REPLYlink written 15 months ago by nichgentry0
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