Question: Problem installing velvet on ubunu 10.04
0
gravatar for Zara
5.3 years ago by
Zara20
Germany
Zara20 wrote:

Dear All,

I'm trying to install velvet on ubuntu 10.04. when I run "make" command I get the following result and finally an error. I don't get any velveth/velvetg executable file and therefore I'm not able to work with velvet.

Can somebody help me in this case please? Thanks :)

==== output of make command : =========

rm obj/*.o obj/dbg/*.o
rm: cannot remove `obj/dbg/*.o': No such file or directory
make: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o
src/splayTable.c: In function ‘scanReferenceSequences’:
src/splayTable.c:877: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
src/splayTable.c:933: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c:949: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1207: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c:1213: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result
gcc -Wall -m64 -O3  -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/../../../libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/../../../libz.a when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [velveth] Error 1

 

ubuntu velvet install assembly • 2.0k views
ADD COMMENTlink modified 5.3 years ago • written 5.3 years ago by Zara20

this is a deleted comment.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Zara20
3
gravatar for Zhaorong
5.3 years ago by
Zhaorong1.2k
State College, PA
Zhaorong1.2k wrote:

It complained about "/usr/bin/ld: cannot find -lz".

Looks like this may be of help.

Briefly, try

sudo apt-get install libz-dev

or 

sudo apt-get install lib32z1-dev

ADD COMMENTlink written 5.3 years ago by Zhaorong1.2k

Thanks a lot for your reply.

I get this result after running the commands, and the problem is still there:

 

root@ali-desktop:~/NGS/velvet_1.2.10# sudo apt-get install libz-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Note, selecting zlib1g-dev instead of libz-dev
zlib1g-dev is already the newest version.
The following packages were automatically installed and are no longer required:
  libmpich2-1.2 libmpich2-dev
Use 'apt-get autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
root@ali-desktop:~/NGS/velvet_1.2.10# sudo apt-get install lib32z1-dev
Reading package lists... Done
Building dependency tree       
Reading state information... Done
E: Couldn't find package lib32z1-dev

 

root@ali-desktop:~/NGS/velvet_1.2.10# make
rm obj/*.o obj/dbg/*.o
rm: cannot remove `obj/dbg/*.o': No such file or directory
make: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o
src/splayTable.c: In function ‘scanReferenceSequences’:
src/splayTable.c:877: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
src/splayTable.c:933: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c:949: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1207: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
src/splayTable.c:1213: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/autoOpen.c -o obj/autoOpen.o
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result
gcc -Wall -m64 -O3  -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/autoOpen.o -lz -lm
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/../../../libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/gcc/i486-linux-gnu/4.4.3/../../../libz.a when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.so when searching for -lz
/usr/bin/ld: skipping incompatible /usr/lib/libz.a when searching for -lz
/usr/bin/ld: cannot find -lz
collect2: ld returned 1 exit status
make: *** [velveth] Error 1

ADD REPLYlink written 5.3 years ago by Zara20
1

Try 

sudo apt-get install lib64z1-dev
ADD REPLYlink written 5.3 years ago by Zhaorong1.2k

Thanks a lot :) now make works. But when executable file are generated, I can't run them. Would you please let me know if you have some comments in this case also?

root@ali-desktop:~/NGS/velvet_1.2.10# ./velvetg
bash: ./velvetg: cannot execute binary file

ADD REPLYlink written 5.3 years ago by Zara20
1

See this. Looks like your system is 32-bit? Velvet works only on 64-bit system. See README.txt.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by Zhaorong1.2k

Oh yes exactly. It's a virtual machine I thought it is 64 bit but now after checking I saw it's 32 bit.

Thanks a lot dear Zhaorong.

ADD REPLYlink written 5.3 years ago by Zara20
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