SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
TopHat Error: Could not find Bowtie index files /bowtie-0.12.5/indexes/. rebrendi Bioinformatics 11 06-22-2016 09:55 AM
bwa aln - fail to locate index Geethathanu Bioinformatics 6 12-14-2015 10:38 AM
bwa_sai2sam_pe fail to locate the index alig Bioinformatics 8 03-19-2015 12:40 PM
Could not locate a Bowtie index corresponding to basename YKY Bioinformatics 8 12-29-2014 06:12 AM
bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM

Reply
 
Thread Tools
Old 01-17-2018, 08:28 PM   #1
ng1812
Junior Member
 
Location: california

Join Date: Jan 2018
Posts: 1
Default Could not locate a bowtie index corresponding to basename -- tried posted solutions

Hi,

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.
Code:
bowtie2 index:
/user/home/Downloads/mm10/mm10
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/fastq_to_sams.py", line 92, in <module>
    py_bowtie_single_end('/home/user/phd/NGYHF03', list_output_sam = outputs, bowtie2_index = mm10)
  File "/home/user/phd/fastq_to_sams.py", line 87, in py_bowtie_single_end
    check_output(temp_str, shell=True)
  File "/home/user/anaconda3/lib/python3.6/subprocess.py", line 336, in check_output
    **kwargs).stdout
  File "/home/user/anaconda3/lib/python3.6/subprocess.py", 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?
ng1812 is offline   Reply With Quote
Reply

Tags
alignment, bowtie2, error, index

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 07:18 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO