Bowtie2 on MingW Msys

[BmoreHawk]

Downloaded MinGW and compiled bowtie2 on Msys after switching the /etc/fstab file to 64 bit mode, apparently obtained all the executables. Tried to build the indexes from the fasta file, apparently made it.

When I run the bowtie2 wrapper on this command:

$ bowtie2 -x pathtobowtie2Indexedfolder/indexprefix -1 Fastqm1gz -2 Fastqm2gz > output.sam

the output message is :

POSIX::mkfifo not implemented on this architecture at C:/MinGW/msys/home/user/bowtie2.2.3/bowtie2 line 338

Any suggestion ?

[WhatsOEver]

Well, they say it quite clearly on their website, don't they?

MinGW, being Minimalist, does not, and never will, attempt to provide a POSIX runtime environment for POSIX application deployment on MS-Windows. If you want POSIX application deployment on this platform, please consider Cygwin instead.

[Brian Bushnell]

Or, you could use a program that runs on Windows without an emulation layer, like BBMap.