BWA installation failed after "make" command in Linux

rzeng · 09-04-2013, 03:26 PM

I am the first to install BWA and never use this software by commands of Linux.When I try to install BWA under bwa.0.7.5a, after I typed "make" it showed as follows:

gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread
ld: can't open output file for writing: bwa, errno=21
collect2: ld returned 1 exit status
make: *** [bwa] Error 1

I have installed xcode 3.2.6 on my mac but do not know what's going on there. Anyone can answer my question?

Very appreciate!

lindenb · 09-04-2013, 03:53 PM

cross posted on biostar: http://www.biostars.org/p/80556

GenoMax · 09-05-2013, 04:04 AM

Check to make sure that the account you are running this from has write permissions in this directory hierarchy.

Other thing to check (as posted by someone on biostars) is to see if you already have a file/directory named bwa.

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09-04-2013, 03:26 PM	#1
rzeng Member Location: houston Join Date: Aug 2013 Posts: 19	BWA installation failed after "make" command in Linux I am the first to install BWA and never use this software by commands of Linux.When I try to install BWA under bwa.0.7.5a, after I typed "make" it showed as follows: gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS QSufSort.o bwt_gen.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o is.o bwtindex.o bwape.o kopen.o pemerge.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread ld: can't open output file for writing: bwa, errno=21 collect2: ld returned 1 exit status make: *** [bwa] Error 1 I have installed xcode 3.2.6 on my mac but do not know what's going on there. Anyone can answer my question? Very appreciate!

09-04-2013, 03:53 PM	#2
lindenb Senior Member Location: France Join Date: Apr 2010 Posts: 143	cross posted on biostar: http://www.biostars.org/p/80556

09-05-2013, 04:04 AM	#3
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	Check to make sure that the account you are running this from has write permissions in this directory hierarchy. Other thing to check (as posted by someone on biostars) is to see if you already have a file/directory named bwa.