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Old 05-11-2011, 06:13 AM   #41
Thorondor
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on the oases malinglist Daniel Zerbino wrote:
"Are you compiling Oases with the OPENMP flag? This indeed is not allowed
by the Oases Makefile, as Oases will not be accelerated by the parallel
sections of Velvet (since they are Velvet specific)."

feel free to add to the oases mailinglist:
http://listserver.ebi.ac.uk/mailman/...fo/oases-users
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Old 06-15-2011, 07:08 AM   #42
Apexy
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Hi Oliviera,
Please pardon my ignorance and it this respond is coming late as I started using oases only recently. I wonder if there is a multi-threaded version of oases implementing openmpi at this stage. I looked at the README.txt and did not see openmpi at compilation. If there is some documentation relating to oases and openmpi, I would very much cherish you refer me to. It could be the reason while compilation is unsuccessful with 'OPENMP=1' argument
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Old 06-15-2011, 07:13 AM   #43
Apexy
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Oops! I noticed Thorondor gave a respond already
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Old 06-26-2011, 03:53 PM   #44
catfisher
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Hi, Brett
Have you figured out the problem that Oases inserts Ns and possible ways to avoid them? I encountered the same problem, and I saw that there is an option for scaffolding in Oases, I set it as 'no', but still got contigs with a lot of N's inserted in them. Not sure if you have figured out this problem, or someone else did, thanks
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Old 06-28-2011, 03:11 AM   #45
Thorondor
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yup, this happens also for me, scaffolding is off per default in oases and but you still get this Ns because oases still connect read pairs.

zerbino wrote over oases mailinglist:
"scaffolding only means that you allow Velvet/Oases to take a leap of
faith. Paired-end information is always used in Oases (when available,
of course)."
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Old 07-26-2011, 10:23 AM   #46
shengandy
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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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Old 07-27-2011, 08:34 AM   #47
shengandy
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Default 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
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Old 12-15-2011, 07:27 PM   #48
upendra_35
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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.
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Old 12-16-2011, 07:54 AM   #49
MarcelS
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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,
Marcel
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Old 02-29-2012, 12:42 AM   #50
Nol
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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' ?

Thanks
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Old 02-29-2012, 12:58 AM   #51
Nol
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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 troubles
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Old 02-29-2012, 06:27 AM   #52
Apexy
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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,

Mbandi
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Old 02-29-2012, 11:03 AM   #53
MarcelS
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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,
Marcel
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Old 09-10-2014, 07:09 AM   #54
sanjaysingh765
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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 please
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Old 02-04-2017, 02:13 AM   #55
smurmu
Junior Member
 
Location: new delhi

Join Date: Oct 2016
Posts: 6
Default 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.
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Old 02-06-2017, 12:17 AM   #56
schmima
Member
 
Location: Zrich

Join Date: Apr 2010
Posts: 56
Default

Hi

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


https://github.com/MWSchmid/ABI_SOLiD_software_mirror


Send me a private message for the password to unpack the archives.
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Old 02-06-2017, 08:24 PM   #57
smurmu
Junior Member
 
Location: new delhi

Join Date: Oct 2016
Posts: 6
Default ABI SOLiD software

Quote:
Originally Posted by schmima View Post
Hi

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


https://github.com/MWSchmid/ABI_SOLiD_software_mirror


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.
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Old 02-06-2017, 11:22 PM   #58
schmima
Member
 
Location: Zrich

Join Date: Apr 2010
Posts: 56
Default

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?
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Old 02-07-2017, 09:48 AM   #59
smurmu
Junior Member
 
Location: new delhi

Join Date: Oct 2016
Posts: 6
Default ABI SOLiD SOFTWARE

Quote:
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 murmu.sneha22@gmail.com. You can send me the password in my e-mail id. Thank you once again.
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