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!
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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, ShengandyComment
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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
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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,
MarcelComment
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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' ?
ThanksComment
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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 troublesComment
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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,
MbandiComment
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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,
MarcelComment
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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 pleaseComment
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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
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Hi
I still have some of the old software. I uploaded it here:
Send me a private message for the password to unpack the archives.Comment
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ABI SOLiD software
Thank you so much. It will be a great help for me. I've sent you a mail.Originally posted by schmima View PostHi
I still have some of the old software. I uploaded it here:
Send me a private message for the password to unpack the archives.Comment
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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
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ABI SOLiD SOFTWARE
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.Originally posted by schmima View PostComment
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CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).
Despite this, “CRISPR helped turn genome editing from a specialized technique into...07-31-2026, 11:01 AM -
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM
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