Question: bowtie-2 build error
0
gravatar for NGS-Newbie
2.6 years ago by
NGS-Newbie10
NGS-Newbie10 wrote:

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.

bowtie2-build error • 1.6k views
ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by NGS-Newbie10
2

Try running with --debug and / or --verbose. And use linux.

ADD REPLYlink written 2.6 years ago by h.mon29k

Thanks, h.mon!

I am trying to figure out if I could use it at all on windows.

ADD REPLYlink written 2.6 years ago by NGS-Newbie10
1

Unless there really is a reason that you are not allowed to use Linux you are only making it more painful for yourself.

ADD REPLYlink written 2.6 years ago by WouterDeCoster42k

Thank you WouterDeCoster!

Would there be any workarounds? MinGW (as I understand this is a minimalist version of CygWin) or Ubuntu?

ADD REPLYlink written 2.6 years ago by NGS-Newbie10
1

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".

ADD REPLYlink written 2.6 years ago by h.mon29k
1

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.

ADD REPLYlink written 2.6 years ago by WouterDeCoster42k

Use the bash shell built into Win10. If you don't want to use a real unix distro or a VM.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax76k

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).

ADD REPLYlink written 2.6 years ago by WouterDeCoster42k
2

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.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by genomax76k
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