Indexing a reference genome

Question

[maxgen]

I am Mac user trying to run Bowtie on the example data provided in bowtie manual. When I am trying to index the genome file I am getting the following error: Script is:

cd ~ /Users/Desktop/data/bowtie2 
/Users/Anu/Desktop/data/bowtie2/bowtie2-build /Users/Desktop/data/bowtie2/example/reference/lambda_virus.fa 

Error is:
Traceback (most recent call last):
  File "/Users/Anu/Desktop/data/bowtie2/bowtie2-build", line 95, in <module>
    main()
  File "/Users/Anu/Desktop/data/bowtie2/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 8] Exec format error

Help is appreciated

[GenoMax]

Is lambda_virus.fa in fasta fomat? Add a base name for your index at the end of the command line. Try

/Users/Anu/Desktop/data/bowtie2/bowtie2-build -f /Users/Desktop/data/bowtie2/example/reference/lambda_virus.fa lambda

[maxgen]

Still the same error lambda_virus is in fasta format.....

[ablanchetcohen]

In addition to the missing base name, as indicated by GenoMax2, your path is wrong. The path to your reference fasta file cannot be /Users/Desktop/data.

I would do the following troubleshooting steps. 1. Correct the path. 2. Add the base name, as suggested by genomax2. 3. Check if you have the latest version of Bowtie2. 4 If you still have problems, copy paste here the Bowtie2 version, the command and the error.

[jotan]

Have you installed and compiled Bowtie2?

The error looks like it might be coming from the OS rather than from Bowtie2.

[GenoMax]

Since the bowtie2-build seems to be present the error may actually be due an executable that was compiled for a different OS. @maxgen: You may have downloaded linux executables (you appear to be using Mac OS).

[ablanchetcohen]

Congrats. Pretty sure you found the bug in maxgen's command. I was able to reproduce exactly the same error message on my Mac, by trying to run the Bowtie for Linux.

I'm not really sure why there is a python script calling a C++ program, but the initial bowtie-2-build Python script runs fine initially. It fails at line 92 when it tries to run the C++ program, which was probably compiled for Linux, and not Mac.

---

blancha@hai04 ~/Downloads/bowtie2-2.2.9$ bowtie2-build Traceback (most recent call last): File "./bowtie2-build", line 95, in <module> main() File "./bowtie2-build", line 92, in main os.execv(build_bin_spec, argv) OSError: [Errno 8] Exec format error

Answer 1

[WouterDeCoster]

The index will be created in the current directory, do you have write permissions?