Velvet 1.2.03 install/make error

[nposnien]

Dear all,

I'm trying to install Velvet with non-default Compilation settings, but I get a error:

make
rm obj/*.o obj/dbg/*.o
rm: cannot remove `obj/dbg/*.o': No such file or directory
make: [cleanobj] Error 1 (ignored)
mkdir -p obj
gcc -Wall -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
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
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/graph.c -o obj/graph.o
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
src/graphStats.c: In function 'collectReferenceCoords':
src/graphStats.c:1961: warning: format '%ld' expects type 'long int', but argument 3 has type 'long long int'
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/binarySequences.c -o obj/binarySequences.o
src/binarySequences.c: In function 'importCnyReadSet':
src/binarySequences.c:301: warning: cast from pointer to integer of different size
src/binarySequences.c:301: warning: cast from pointer to integer of different size
src/binarySequences.c:301: warning: format '%lx' expects type 'long unsigned int', but argument 2 has type 'long long unsigned int'
src/binarySequences.c:301: warning: format '%ld' expects type 'long int', but argument 3 has type 'long long unsigned int'
src/binarySequences.c:301: warning: format '%lx' expects type 'long unsigned int', but argument 4 has type 'long long unsigned int'
src/binarySequences.c: In function 'moveCnySeqNucleotides':
src/binarySequences.c:386: warning: format '%ld' expects type 'long int', but argument 2 has type 'uint64_t'
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/shortReadPairs.c -o obj/shortReadPairs.o
gcc -Wall -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=2 -c src/locallyCorrectedGraph.c -o obj/locallyCorrectedGraph.o
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
src/preGraphConstruction.c: In function 'createPreNodes':
src/preGraphConstruction.c:525: warning: format '%ld' expects type 'long int', but argument 2 has type 'long long unsigned int'
src/preGraphConstruction.c:525: warning: format '%ld' expects type 'long int', but argument 3 has type 'long long unsigned int'
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 -o velveth obj/tightString.o obj/run.o obj/recycleBin.o obj/splay.o obj/splayTable.o obj/readSet.o obj/binarySequences.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o -lz -lm
gcc -Wall -O3 -o velvetg obj/tightString.o obj/graph.o obj/run2.o obj/fibHeap.o obj/fib.o obj/concatenatedGraph.o obj/passageMarker.o obj/graphStats.o obj/correctedGraph.o obj/dfib.o obj/dfibHeap.o obj/recycleBin.o obj/readSet.o obj/binarySequences.o obj/shortReadPairs.o obj/scaffold.o obj/locallyCorrectedGraph.o obj/graphReConstruction.o obj/roadMap.o obj/preGraph.o obj/preGraphConstruction.o obj/concatenatedPreGraph.o obj/readCoherentGraph.o obj/utility.o obj/kmer.o obj/kmerOccurenceTable.o obj/allocArray.o -lz -lm

A google search gives this post for another Version of Velvet. But I was not able to solve the problem.
I installed zlib 1.2.3 from the Velvet folder (make in zlib folder). Still nothing worked.

The Remotecomputer I use runs with SuSE.

I would appreciate any help!

Thank you!

[nposnien]

Problem is solved. The error can be ignored.

[shrujan]

How the problem is solved ??

Hi,

This is Shrujan kumar Madadha, i am facing the same kind of error what kind of error you have faced before. But you have mentioned that it was resolved may i please know how it was resolved.

when i gave a velvetg or velveth command it is giving an error. The following is the problem :

shrujan@ubuntu:~/NGS_Practice/Staphylococcus/Assembly$ ~/Programs/velvet_1.2.08 /./velvetg Kmer_71 -ins_length 200 -ins_length_sd 50 -scaffolding yes -cov_cutoff10 -min_contig_lgth 300 -read_trkg yes
bash: /home/shrujan/Programs/velvet_1.2.08: No such file or directory

So please guide me with the valuable solutions.

Thank you and i hope for a quick reply.
Shrujan kumar Madadha.

[mastal]

to run velvetg:

$ ~/Programs/velvet_1.2.08/velvetg

followed by the parameters. You had an extra '/.' in there.

But unless you have installed velvet by running make, you won't have the velveth and velvetg programs in the velvet directory, which could be why you are getting the error message 'No such file or directory.'

[shrujan]

i have installed velvet and typed make it compiled perfectly but i couldn't understand your reply, whether i have to add /. in that command if so where should i ???

[shrujan]

if i remove that extra /. also i am getting the same error as mentioned,

[mastal]

Are you specifying the path to the velvet directory correctly?

Try just running velveth or velvetg without any parameters, if velvet is compiled correctly, you should get the help message.

For example:

$ /home/shrujan/Programs/velvet_1.2.08/velveth