Announcement

Collapse
No announcement yet.
X
Collapse
 
  • Page of 4
  • Filter
  • Time
  • Show
Clear All
new posts
Previous 1 2 3 4 template Next
  • #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

    • #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

      • #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

        • #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

          • #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

            • #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

              • #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

                • #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...ts094.abstract

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

                  Regards,
                  Marcel

                  Comment

                  • #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

                    • #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

                      • #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

                        • #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

                          • #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

                            • #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

                              Previous 1 2 3 4 template Next

                              Latest Articles

                              Collapse
                              • seqadmin
                                Advanced Methods for the Detection of Infectious Disease
                                by seqadmin




                                The recent pandemic caused worldwide health, economic, and social disruptions with its reverberations still felt today. A key takeaway from this event is the need for accurate and accessible tools for detecting and tracking infectious diseases. Timely identification is essential for early intervention, managing outbreaks, and preventing their spread. This article reviews several valuable tools employed in the detection and surveillance of infectious diseases.
                                ...
                                11-27-2023, 01:15 PM
                              • seqadmin
                                Strategies for Investigating the Microbiome
                                by seqadmin




                                Microbiome research has led to the discovery of important connections to human and environmental health. Sequencing has become a core investigational tool in microbiome research, a subject that we covered during a recent webinar. Our expert speakers shared a number of advancements including improved experimental workflows, research involving transmission dynamics, and invaluable analysis resources. This article recaps their informative presentations, offering insights...
                                11-09-2023, 07:02 AM
                              View All

                              ad_right_rmr

                              Collapse

                              News

                              Collapse
                              Topics Statistics Last Post
                              Non-Invasive DNA Analysis: A New Tool for Monitoring Polar Bears by seqadmin
                              Started by seqadmin, 12-05-2023, 02:24 PM
                              0 responses
                              13 views
                              0 likes
                              		 Last Post seqadmin
                              by seqadmin
                              12-05-2023, 02:24 PM  
                              Innovative Technique Enhances Understanding of Gene Regulation by seqadmin
                              Started by seqadmin, 12-05-2023, 07:37 AM
                              0 responses
                              25 views
                              0 likes
                              		 Last Post seqadmin
                              by seqadmin
                              12-05-2023, 07:37 AM  
                              New Cultivars on the Horizon: Over 100 Magic Mushroom Genomes Analyzed by seqadmin
                              Started by seqadmin, 12-04-2023, 08:23 AM
                              0 responses
                              9 views
                              0 likes
                              		 Last Post seqadmin
                              by seqadmin
                              12-04-2023, 08:23 AM  
                              Single-Cell Sequencing: A New Era in Understanding Genetic Developmental Disorders by seqadmin
                              Started by seqadmin, 12-01-2023, 09:55 AM
                              0 responses
                              25 views
                              0 likes
                              		 Last Post seqadmin
                              by seqadmin
                              12-01-2023, 09:55 AM  
                              View All
                              Working...
                              X