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  • jellybaby83
    Member
    • Jul 2014
    • 10
    #1

    Velvet compiling

    Hi all.

    I have been using velvet (and it was woriking fine) but I would like to increase the Kmer length. I keep getting a message like the following:

    Code:
    shell@shell-MS-1727:/mnt/velvet_1.2.10$ sudo make ’BUNDLEDZLIB=1’ ’MAXKMERLENGTH=57’
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 ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1060:14: warning: variable ‘refElem’ set but not used [-Wunused-but-set-variable]
      RefInfo refElem;
              ^
src/splayTable.c: In function ‘scanReferenceSequences’:
src/splayTable.c:877:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c: In function ‘scanBinaryReferenceSequences’:
src/splayTable.c:933:8: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
   fgets(line, MAXLINE, file);
        ^
src/splayTable.c:949:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, file);
         ^
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:1207:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
src/splayTable.c:1213:11: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
      fgets(line, MAXLINE, seqFile);
           ^
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 
src/readSet.c: In function ‘readFastXFile’:
src/readSet.c:641:21: warning: assignment from incompatible pointer type [enabled by default]
         file.gzFile = file.autoFile = NULL;
                     ^
src/readSet.c: In function ‘readFastXPair’:
src/readSet.c:680:22: warning: assignment from incompatible pointer type [enabled by default]
         file1.gzFile = file1.autoFile = NULL;
                      ^
src/readSet.c:681:22: warning: assignment from incompatible pointer type [enabled by default]
         file2.gzFile = file2.autoFile = NULL;
                      ^
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -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 -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 ‘pcloseNoStderr’:
src/autoOpen.c:49:6: warning: variable ‘rc’ set but not used [-Wunused-but-set-variable]
  int rc, status;
      ^
src/autoOpen.c: In function ‘popenNoStderr’:
src/autoOpen.c:28:6: warning: ignoring return value of ‘dup’, declared with attribute warn_unused_result [-Wunused-result]
   dup(out[1]);
      ^
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
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 -lz -lm
    I have tried installing velvet from scratch again. I have updated the zlib using the following:

    Code:
    sudo apt-get install zlib1g-dev
    I have checked the make file states:

    LIBS = -lm

    as suggested elsewere on this forum

    some problems installing velvet - SEQanswers
    http://seqanswers.com/forums/showthread.php?t=31396
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc


    Nothing I have read/tried has worked.
    Tags: None
    • Naibin Duan
      Junior Member
      • Jan 2014
      • 4
      #2
      I am finding the same question.

      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 ‘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 -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
      src/readSet.c: In function ‘readFastXFile’:
      src/readSet.c:641:21: warning: assignment from incompatible pointer type [enabled by default]
      file.gzFile = file.autoFile = NULL;
      ^
      src/readSet.c: In function ‘readFastXPair’:
      src/readSet.c:680:22: warning: assignment from incompatible pointer type [enabled by default]
      file1.gzFile = file1.autoFile = NULL;
      ^
      src/readSet.c:681:22: warning: assignment from incompatible pointer type [enabled by default]
      file2.gzFile = file2.autoFile = NULL;
      ^
      gcc -Wall -m64 -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -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 -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 ‘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 -lz -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 -lz -lm


      the bolded out wors were the main problom ....... hope some can know the answer .

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