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: /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?