Velvet Installation Headache

Question

[richardschumaker126]

Hello all,

I'm trying to install Velvet 1.2.10 on an HPC. I keep running into the same problem during the "make" step. Below are the error messages:

rm obj/*.o obj/dbg/*.o 
rm: cannot remove ‘obj/dbg/*.o’: No such file or directory
make: [cleanobj] Error 1 (ignored)
cd third-party/zlib-1.2.3; ./configure; make; rm minigzip.o; rm example.o
Checking for gcc...
Building static library libz.a version 1.2.3 with gcc.
Checking for unistd.h... Yes.
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf()
Checking for vsnprintf() in stdio.h... Yes.
Checking for return value of vsnprintf()... Yes.
Checking for errno.h... Yes.
Checking for mmap support... Yes.
make[1]: Entering directory `/data/cahnrs/lange/velvet_assembly/velvet_1.2.10/third-party/zlib-1.2.3'
gcc -O3 -DUSE_MMAP   -c -o example.o example.c
gcc -O3 -DUSE_MMAP   -c -o adler32.o adler32.c
gcc -O3 -DUSE_MMAP   -c -o compress.o compress.c
gcc -O3 -DUSE_MMAP   -c -o crc32.o crc32.c
gcc -O3 -DUSE_MMAP   -c -o gzio.o gzio.c
gcc -O3 -DUSE_MMAP   -c -o uncompr.o uncompr.c
gcc -O3 -DUSE_MMAP   -c -o deflate.o deflate.c
gcc -O3 -DUSE_MMAP   -c -o trees.o trees.c
gcc -O3 -DUSE_MMAP   -c -o zutil.o zutil.c
gcc -O3 -DUSE_MMAP   -c -o inflate.o inflate.c
gcc -O3 -DUSE_MMAP   -c -o infback.o infback.c
gcc -O3 -DUSE_MMAP   -c -o inftrees.o inftrees.c
gcc -O3 -DUSE_MMAP   -c -o inffast.o inffast.c
ar rc libz.a adler32.o compress.o crc32.o gzio.o uncompr.o deflate.o trees.o zutil.o inflate.o infback.o inftrees.o inffast.o 
gcc -O3 -DUSE_MMAP -o example example.o -L. libz.a
gcc -O3 -DUSE_MMAP   -c -o minigzip.o minigzip.c
gcc -O3 -DUSE_MMAP -o minigzip minigzip.o -L. libz.a
make[1]: Leaving directory `/data/cahnrs/lange/velvet_assembly/velvet_1.2.10/third-party/zlib-1.2.3'
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/tightString.c -o obj/tightString.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/run.c -o obj/run.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/splay.c -o obj/splay.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/splayTable.c -o obj/splayTable.o 
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1060:14: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
      RefInfo refElem;
              ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/graph.c -o obj/graph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/run2.c -o obj/run2.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/fib.c -o obj/fib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/dfib.c -o obj/dfib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/readSet.c -o obj/readSet.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/binarySequences.c -o obj/binarySequences.o 
src/binarySequences.c: In function ‘importCnyReadSet’:
src/binarySequences.c:314:12: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
    RefInfo refElem;
            ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/shortReadPairs.c -o obj/shortReadPairs.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/utility.c -o obj/utility.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/kmer.c -o obj/kmer.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -D BUNDLEDZLIB -c src/autoOpen.c -o obj/autoOpen.o 
src/autoOpen.c: In function ‘pcloseNoStderr’:
src/autoOpen.c:49:6: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
  int rc, status;
      ^
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 third-party/zlib-1.2.3/*.o -lm
gcc -Wall -m64 -O3  -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o obj/autoOpen.o third-party/zlib-1.2.3/*.o -lm

Here is what I've tried: 1) Loading an older gcc version (4.9.3) 2) Using the command make 'BUNDLEDZLIB=1' 3) Making sure the makefile had -lm at the end of the cc -Wall -O3 -o velvetg obj/tightString.o ... -lm (of course all in variables now $LIBS)

Nothing has worked so far. Any suggestions would be appreciated!

Richard

[GenoMax]

Those are just warning messages. Are you sure the program has not compiled? (may need to look in sub-directories e.g. src/bin)

[richardschumaker126]

It looks like velveth worked despite the warning messages. Thank you!

Answer 1

[k.kathirvel93]

Did you set a K mer length while installation? If not, Use emacs and edit your make file, then it will work.