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  • shengandy
    Junior Member
    • Jun 2011
    • 3
    #46
    Can anyone tell me how to compile velveth in linux. I want to change the 'MAXKMERLENGTH' value to 57 for the assembly. Do I need to download other software for this? Thanks a lot!

    Comment

    • shengandy
      Junior Member
      • Jun 2011
      • 3
      #47
      where to find velvet 1.1.03

      I downloaded velvet 1.1.04 and tried to compiled it with 'MAXKMERLENGTH=57'. I got the error information that "obj/dbg/* files not found. I checked the folder. There were *.o files in the folder obj and no files in the folder obj/dbg/. Then I downloaded the file again. This time there were no files in either obj/ folder and obj/dbg/ folder. I wondered if I should download velvet 1.1.03. But I could not find it. Any suggestions? Thanks, Shengandy

      Comment

      • upendra_35
        Senior Member
        • Apr 2010
        • 102
        #48
        Do any of you guys know how long does the velvetg takes to denovo assemble PE reads from 3 lanes (~70million reads/lane). The velveth was quick but velvetg has been running on one processor for the last 106 hours. Please advise whether i have to keep it going or kill and start a fresh job.

        Comment

        • MarcelS
          Junior Member
          • Feb 2010
          • 5
          #49
          Hi,
          if velvety runs that long for 70 Mio reads, that normally means that you ran out of main memory and the computer uses swap memory which takes very long. you can check that on the machine using the unix tools top or free.
          You can have a look at the new Manual at the oases webpage (since version 0.2 http://www.ebi.ac.uk/~zerbino/oases/), which contains advice if you run into memory problems.

          Regards,
          Marcel

          Comment

          • Nol
            Junior Member
            • Jul 2011
            • 3
            #50
            Hi all.

            recently, oases 0.2 was released and it is now able to deal with multiple kmers assembly. I was so happy when I found out that I compiled it immediately.
            Unfortunately, it did not want to compile with the MAXKMERLENGTH I provided...
            I used:

            make 'VELVET_DIR=/home/velvet_1.2.02' 'MAXKMERLENGHT=61' 'OPENMP=1'

            and it replied:

            rm -f obj/*.o obj/dbg/*.o
            cd /home/velvet_1.2.02&& make obj
            make[1]: entrant dans le répertoire « /home/velvet_1.2.02 »
            rm obj/*.o obj/dbg/*.o
            rm: impossible de supprimer « obj/dbg/*.o »: Aucun fichier ou dossier de ce type
            make[1]: [cleanobj] Erreur 1 (ignorée)
            mkdir -p obj
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/binarySequences.c -o obj/binarySequences.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o
            make[1]: quittant le répertoire « /home/velvet_1.2.02 »
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/oases.c -o obj/oases.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/transcript.c -o obj/transcript.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph2.c -o obj/locallyCorrectedGraph2.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/filterTranscripts.c -o obj/filterTranscripts.o -I/home/velvet_1.2.02/src
            gcc -Wall -fopenmp -O3 -o oases obj/oases.o obj/transcript.o obj/scaffold.o obj/locallyCorrectedGraph2.o obj/correctedGraph.o obj/filterTranscripts.o /home/velvet_1.2.02/obj/recycleBin.o /home/velvet_1.2.02/obj/utility.o /home/velvet_1.2.02/obj/graph.o /home/velvet_1.2.02/obj/passageMarker.o /home/velvet_1.2.02/obj/readSet.o /home/velvet_1.2.02/obj/tightString.o /home/velvet_1.2.02/obj/kmer.o /home/velvet_1.2.02/obj/dfibHeap.o /home/velvet_1.2.02/obj/dfib.o /home/velvet_1.2.02/obj/concatenatedGraph.o /home/velvet_1.2.02/obj/graphStats.o /home/velvet_1.2.02/obj/fibHeap.o /home/velvet_1.2.02/obj/fib.o /home/velvet_1.2.02/obj/readCoherentGraph.o /home/velvet_1.2.02/obj/allocArray.o /home/velvet_1.2.02/obj/binarySequences.o -lz -lm

            as a result, for any kmer > 31, velveth and velvetg run normally but oases does not.. we got the error message:

            [dheilly@pbi-cbetm ~]$ oases '/home/dheilly/Bre2_35' -ins_length 200
            [0.000000] Reading graph file /home/dheilly/Bre2_35/Graph2
            oases: Word length 35 greater than max allowed value (31).
            Recompile Velvet to deal with this word length.: Success

            I don't understand. Can anybody help us make oases take into account the option 'MAXKMERLENGTH=61' ?

            Thanks

            Comment

            • Nol
              Junior Member
              • Jul 2011
              • 3
              #51
              Hi all, me again

              I apologize for the message above.

              I just found out that we did not write MAXKMERLENGTH properly...

              here: make 'VELVET_DIR=/home/velvet_1.2.02' 'MAXKMERLENGHT=61' 'OPENMP=1'

              I wish oases had pointed out that we did not write it properly... we wasted a week for .. nothing really!

              anyway. problem solved!!! sorry for the troubles

              Comment

              • Apexy
                Member
                • Apr 2011
                • 62
                #52
                Hello Nol,

                Out of curiosity, I am wondering why you had to compile oases with 'OPENMP=1'. Is oases now multi-threaded?. Kindly let me know as I have always understood it was only a few steps in velvet that are multi-threaded.

                Cheers,

                Mbandi

                Comment

                • MarcelS
                  Junior Member
                  • Feb 2010
                  • 5
                  #53
                  Hello everyone,
                  I just wanted to point out that we published the Oases paper now and if you are interested in more details, also how to set parameters, please have a look:

                  http://bioinformatics.oxfordjournals.org/content/early/2012/02/24/bioinformatics.bts094.abstract


                  Concerning Mbandis question, no Oases is not multithreaded yet. There is no difference if you compile Oases with 'OPENMP=1'.

                  Regards,
                  Marcel

                  Comment

                  • sanjaysingh765
                    Junior Member
                    • Jun 2011
                    • 5
                    #54
                    Hi all,
                    I am trying to install the velvet_1.2.10 and oases_0.2.8 on UBUNTU 14.0 server and got this error
                    Code:
                    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 `/home/sanjay/Desktop/velvet_1.1.02/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 `/home/sanjay/Desktop/velvet_1.1.02/third-party/zlib-1.2.3'
mkdir -p obj
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
src/run.c: In function ‘main’:
src/run.c:197:10: warning: ignoring return value of ‘system’, declared with attribute warn_unused_result [-Wunused-result]
    system(buf);
          ^
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/splayTable.c -o obj/splayTable.o 
src/splayTable.c: In function ‘computeClearHSPs’:
src/splayTable.c:631:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, seqFile);
         ^
src/splayTable.c: In function ‘inputSequenceArrayIntoSplayTableAndArchive’:
src/splayTable.c:931:9: warning: ignoring return value of ‘fgets’, declared with attribute warn_unused_result [-Wunused-result]
    fgets(line, MAXLINE, seqFile);
         ^
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o 
src/graph.c: In function ‘addBufferToDescriptor’:
src/graph.c:791:14: warning: variable ‘twinDescr’ set but not used [-Wunused-but-set-variable]
  Descriptor *twinDescr;
              ^
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readSet.c -o obj/readSet.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
src/shortReadPairs.c: In function ‘pushNeighbours’:
src/shortReadPairs.c:885:8: warning: variable ‘lastCandidate’ set but not used [-Wunused-but-set-variable]
  Node *lastCandidate = NULL;
        ^
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
src/locallyCorrectedGraph.c: In function ‘tourBusNode_local’:
src/locallyCorrectedGraph.c:380:8: warning: variable ‘destination’ set but not used [-Wunused-but-set-variable]
  Node *destination;
        ^
src/locallyCorrectedGraph.c: In function ‘clipTipsVeryHardLocally’:
src/locallyCorrectedGraph.c:427:18: warning: variable ‘twin’ set but not used [-Wunused-but-set-variable]
  Node *current, *twin;
                  ^
src/locallyCorrectedGraph.c: In function ‘correctGraphLocally’:
src/locallyCorrectedGraph.c:517:8: warning: variable ‘index’ set but not used [-Wunused-but-set-variable]
  IDnum index, nodeIndex;
        ^
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -O3 -lm -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o third-party/zlib-1.2.3/*.o
gcc -Wall -O3 -lm -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/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 third-party/zlib-1.2.3/*.o
obj/graphStats.o: In function `exportAMOSContigs':
graphStats.c:(.text+0x3e68): undefined reference to `sqrt'
obj/scaffold.o: In function `projectFromLongRead':
scaffold.c:(.text+0x10b1): undefined reference to `sqrt'
obj/scaffold.o: In function `projectFromShortRead':
scaffold.c:(.text+0x17b8): undefined reference to `sqrt'
scaffold.c:(.text+0x17d2): undefined reference to `sqrt'
obj/scaffold.o: In function `buildScaffold':
scaffold.c:(.text+0x2d2c): undefined reference to `exp'
scaffold.c:(.text+0x2d55): undefined reference to `exp'
scaffold.c:(.text+0x2d72): undefined reference to `erf'
scaffold.c:(.text+0x2d95): undefined reference to `erf'
scaffold.c:(.text+0x2dbc): undefined reference to `erf'
scaffold.c:(.text+0x2de9): undefined reference to `exp'
scaffold.c:(.text+0x2e1c): undefined reference to `exp'
scaffold.c:(.text+0x2e3d): undefined reference to `erf'
scaffold.c:(.text+0x3608): undefined reference to `sqrt'
scaffold.c:(.text+0x361a): undefined reference to `sqrt'
scaffold.c:(.text+0x363b): undefined reference to `sqrt'
collect2: error: ld returned 1 exit status
make: *** [velvetg] Error 1
sanjay@sanjay:~/Desktop/velvet_1.1.02$ cd ..
sanjay@sanjay:~/Desktop$ cd oases_0.2.8/
sanjay@sanjay:~/Desktop/oases_0.2.8$ make 'VELVET_DIR=~/Desktop/velvet_1.2.10' 'MAXKMERLENGTH=57'
rm -f obj/*.o obj/dbg/*.o 
cd ~/Desktop/velvet_1.2.10 && make -e obj
make[1]: Entering directory `/home/sanjay/Desktop/velvet_1.2.10'
rm obj/*.o obj/dbg/*.o 
rm: cannot remove ‘obj/dbg/*.o’: No such file or directory
make[1]: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/run.c -o obj/run.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/splay.c -o obj/splay.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -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=57 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/run2.c -o obj/run2.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/fib.c -o obj/fib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/dfib.c -o obj/dfib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -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=57 -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=57 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/utility.c -o obj/utility.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/kmer.c -o obj/kmer.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -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]);
      ^
make[1]: Leaving directory `/home/sanjay/Desktop/velvet_1.2.10'
gcc -Wall -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=2 -c src/oases.c -o obj/oases.o -I~/Desktop/velvet_1.2.10/src
src/oases.c:25:21: fatal error: globals.h: No such file or directory
 #include "globals.h"
                     ^
compilation terminated.
make: *** [obj/oases.o] Error 1
sanjay@sanjay:~/Desktop/oases_0.2.8$ make 'VELVET_DIR=~/Desktop/velvet_1.2.10' 'MAXKMERLENGTH=57' 'CATEGORIES=5'
rm -f obj/*.o obj/dbg/*.o 
cd ~/Desktop/velvet_1.2.10 && make -e obj
make[1]: Entering directory `/home/sanjay/Desktop/velvet_1.2.10'
rm obj/*.o obj/dbg/*.o 
rm: cannot remove ‘obj/dbg/*.o’: No such file or directory
make[1]: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/tightString.c -o obj/tightString.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/run.c -o obj/run.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/splay.c -o obj/splay.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -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=57 -D CATEGORIES=5 -c src/graph.c -o obj/graph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/run2.c -o obj/run2.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/fibHeap.c -o obj/fibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/fib.c -o obj/fib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/concatenatedGraph.c -o obj/concatenatedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/passageMarker.c -o obj/passageMarker.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/graphStats.c -o obj/graphStats.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/correctedGraph.c -o obj/correctedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/dfib.c -o obj/dfib.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/dfibHeap.c -o obj/dfibHeap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/recycleBin.c -o obj/recycleBin.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -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=57 -D CATEGORIES=5 -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=57 -D CATEGORIES=5 -c src/shortReadPairs.c -o obj/shortReadPairs.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/graphReConstruction.c -o obj/graphReConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/roadMap.c -o obj/roadMap.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/preGraph.c -o obj/preGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/preGraphConstruction.c -o obj/preGraphConstruction.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/concatenatedPreGraph.c -o obj/concatenatedPreGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/readCoherentGraph.c -o obj/readCoherentGraph.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/utility.c -o obj/utility.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/kmer.c -o obj/kmer.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/scaffold.c -o obj/scaffold.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/kmerOccurenceTable.c -o obj/kmerOccurenceTable.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/allocArray.c -o obj/allocArray.o 
gcc -Wall -m64 -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -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]);
      ^
make[1]: Leaving directory `/home/sanjay/Desktop/velvet_1.2.10'
gcc -Wall -O3 -D MAXKMERLENGTH=57 -D CATEGORIES=5 -c src/oases.c -o obj/oases.o -I~/Desktop/velvet_1.2.10/src
src/oases.c:25:21: fatal error: globals.h: No such file or directory
 #include "globals.h"
                     ^
compilation terminated.


                    Can anyone help me out please

                    Comment

                    • smurmu
                      Junior Member
                      • Oct 2016
                      • 6
                      #55
                      velvet assembler

                      Hi...
                      Can anyone please tell me from where I can obtain denovo_preprocessor_solid_v2.2.1.pl and denovo_post_processor_solid_v2.2.1.pl script? I'm working with SOLiD colorspace data and I wish to use an assembler which accepts colorspace reads. After exploring, I came to know about velvet assembler. But to make use of this facility I need that script.
                      I tried opening this site http://www.solidsoftwaretools.com/gf...t/denovotools/ as it was mentioned in a paper but I don't know why its not working.

                      Any help is greatly appreciated.

                      Comment

                      • schmima
                        Member
                        • Apr 2010
                        • 56
                        #56
                        Hi

                        I still have some of the old software. I uploaded it here:


                        GitHub - MWSchmid/ABI_SOLiD_software_mirror: Inofficial mirror/repo for SOLiD legacy software
                        https://github.com/MWSchmid/ABI_SOLiD_software_mirror
                        Inofficial mirror/repo for SOLiD legacy software. Contribute to MWSchmid/ABI_SOLiD_software_mirror development by creating an account on GitHub.



                        Send me a private message for the password to unpack the archives.

                        Comment

                        • smurmu
                          Junior Member
                          • Oct 2016
                          • 6
                          #57
                          ABI SOLiD software

                          Originally posted by schmima View Post
                          Hi

                          I still have some of the old software. I uploaded it here:


                          GitHub - MWSchmid/ABI_SOLiD_software_mirror: Inofficial mirror/repo for SOLiD legacy software
                          https://github.com/MWSchmid/ABI_SOLiD_software_mirror
                          Inofficial mirror/repo for SOLiD legacy software. Contribute to MWSchmid/ABI_SOLiD_software_mirror development by creating an account on GitHub.



                          Send me a private message for the password to unpack the archives.
                          Thank you so much. It will be a great help for me. I've sent you a mail.

                          Comment

                          • schmima
                            Member
                            • Apr 2010
                            • 56
                            #58
                            I did't receive an e-mail on any of my accounts - and somehow I cannot send you a private message on SEQanswers. Did you block your private messaging?

                            Comment

                            • smurmu
                              Junior Member
                              • Oct 2016
                              • 6
                              #59
                              ABI SOLiD SOFTWARE

                              Originally posted by schmima View Post
                              I did't receive an e-mail on any of my accounts - and somehow I cannot send you a private message on SEQanswers. Did you block your private messaging?
                              No, I didn't block. All the setting looks fine to me. Even I'm not able to send you the private message. Here is my mail id [email protected]. You can send me the password in my e-mail id. Thank you once again.

                              Comment

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