Entering edit mode
6.8 years ago
NGS-Newbie
▴
10
Hi All
I am trying to build bowtie index, on Windows 10 using CygWin. Getting the following error when I run - bowtie2-build myfile.fa index_file
Traceback (most recent call last):
File "/usr/local/bin/bowtie2-build", line 95, in <module>
main()
File "/usr/local/bin/bowtie2-build", line 92, in main
os.execv(build_bin_spec, argv)
OSError: [Errno 8] Exec format error
Any ideas on how to fix it?
Thanks so much!
UPDATE: I tried using the prebuilt version of Bowtie2 as well. I get the same error.
Try running with
--debug
and / or--verbose
. And use linux.Thanks, h.mon!
I am trying to figure out if I could use it at all on windows.
Unless there really is a reason that you are not allowed to use Linux you are only making it more painful for yourself.
Thank you WouterDeCoster!
Would there be any workarounds? MinGW (as I understand this is a minimalist version of CygWin) or Ubuntu?
Ubuntu or any other linux distribution. Ubuntu is generally easy to install and use, so it is a commonly used distribution. I personally prefer Xubuntu over Ubuntu. But really, any distribution a friend of yours use is fine, this way, you will have "local support".
I think the most support online is available for Ubuntu, the most common "Linux starter" system (I also use it). The flavor of Linux doesn't really matter.
Use the bash shell built into Win10. If you don't want to use a real unix distro or a VM.
I've never tried bash on Windows10 (or windows10 at all), can you do everything in Win10 Bash now? Because if so I might have to stop windows bashing on biostars (pun intended).
With exception of
fastq-dump
everything else that does not need a GUI works in bash shell on Win10 (ref @Istvan, Win10 bash setup is covered in Biostar handbook). A few programs I tested have worked fine.