Bwa Installation Failed After "Make" Command In Linux

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10.6 years ago

Tonyzeng ▴ 310

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!

bwa • 7.5k views

ADD COMMENT • link updated 10.6 years ago by Istvan Albert 100k • written 10.6 years ago by Tonyzeng ▴ 310

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Check here for the answer. Hint: you have a directory in your current working directory that is named "bwa". Rename that folder and try again.

ADD REPLY • link 10.6 years ago by Matt Shirley 10k

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Why not post this as answer instead of a comment?

ADD REPLY • link 10.6 years ago by Andreas ★ 2.5k

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I'm honestly not trying for snark here. Because it's answered perfectly clearly elsewhere, at several searchable locations, and because answering a question of the format "X" installation failed after "Y" command does not help anyone but the OP.