Question: segemehl installation problem
gravatar for kagan.ferenc
12 months ago by
kagan.ferenc0 wrote:

Hello all, I'm fairly new to bioinformatics and now that I have my own NGS data I started analyse it. I'm over the quality check and now I'd like to map the reads for which I want to use segemehl. Unfortunately I hit a dead end when trying to install it. Tried to look for some solutions online to fix it but could not find anything. Followed every step described by the installation guide (have htslib and all the necessary libraries and gcc) and got the following error:

Linking segemehl cc build/alignment.o build/aluruSort.o build/annotation.o build/bamio.o build/bedfiles.o build/bgzip.o build/biofiles.o build/bitArray.o build/bitVector.o build/bitvectoralg.o build/brendel.o build/charsequence.o build/container.o build/debug.o build/fileBins.o build/filebuffer.o build/fileio.o build/gzidx.o build/gzip.o build/info.o build/intervaltree.o build/iupac.o build/junctions.o build/karlin.o build/kdchain.o build/kdseed.o build/locus.o build/manopt.o build/manout.o build/mapfrag.o build/mappingqual.o build/match.o build/matealign.o build/mathematics.o build/md5.o build/memory.o build/merge.o build/multicharseq.o build/nw.o build/pigeon.o build/portable_endian.o build/queryalign.o build/radixsort.o build/samheader.o build/samio.o build/segemehl_helper.o build/seqclip.o build/sort.o build/splitalign.o build/stack.o build/stringutils.o build/sufarray.o build/sw.o build/vqueue.o build/vstack.o build/vtprogressbar.o build/segemehl.o -o ./segemehl.x -lm -lpthread -lz -lncurses -L libs -lform -lmenu -L/usr/local/lib/ pkg-config --libs htslib "-Wl,-rpath,pkg-config --variable=libdir htslib" Undefined symbols for architecture x86_64: "_hts_set_cache_size", referenced from: _bl_bamOpenFile in bamio.o ld: symbol(s) not found for architecture x86_64 clang: error: linker command failed with exit code 1 (use -v to see invocation) make: * [segemehl] Error 1

Anyone has any idea what is behind it? Thank you in advance.

ADD COMMENTlink written 12 months ago by kagan.ferenc0
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