error with velvet

[RachelWu]

Hello, I download the velvet software package from EBI ( http://www.ebi.ac.uk/~zerbino/velvet/ ). There is an error when I install it.

src / readSet.c: 34:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [obj / readSet.o] Error 1

Who knows what the problem is and how to solve it?
Thanks!

[mandar.sahasrabuddhe]

I too am getting the same error and inspite of trying out changes in path and file name I am unable to install Velvet. Any pointers would be really appreciated.

[ramadatta.88]

problem installing velvet

Hi RachelWu, mandar.sahasrabuddhe

did any of you resolved the problem.PLease let me know.I m new to assembling and i m facing the same error..

src/readSet.c:35:18: error: zlib.h: No such file or directory
src/readSet.c: In function âreadFastQGZFileâ:
src/readSet.c:488: error: âgzFileâ undeclared (first use in this function)
src/readSet.c:488: error: (Each undeclared identifier is reported only once
src/readSet.c:488: error: for each function it appears in.)
src/readSet.c:488: error: expected â;â before âfileâ
src/readSet.c:497: error: âfileâ undeclared (first use in this function)
: :
: :
: :


Thank you.

[arvid]

You need to install zlib-devel (or whatever the equivalent on your server distribution is).

[RachelWu]

Enter the folder which has zlib.h in terminal, run "make".
Then install velvet.

Hi RachelWu, mandar.sahasrabuddhe

did any of you resolved the problem.PLease let me know.I m new to assembling and i m facing the same error..

src/readSet.c:35:18: error: zlib.h: No such file or directory
src/readSet.c: In function âreadFastQGZFileâ:
src/readSet.c:488: error: âgzFileâ undeclared (first use in this function)
src/readSet.c:488: error: (Each undeclared identifier is reported only once
src/readSet.c:488: error: for each function it appears in.)
src/readSet.c:488: error: expected â;â before âfileâ
src/readSet.c:497: error: âfileâ undeclared (first use in this function)
: :
: :
: :


Thank you.

[Biomicrogen]

zlib error as well

I am having the same error on Ubuntu 12. I installed the zlib with the make command with no errors, but I still get the same no zlib.h file found. I ensured the velvet makefile was pointed to the correct path and still compiling error. No velveth or velvetg files created. Ubuntu does have an older version of velvet which it will install correctly which I can use, however it installs with the default kmer=31. How can I recompile this velvet version with a custom kmer value? Please help! Thanks!

[Torst]

Hello, I download the velvet software package from EBI ( http://www.ebi.ac.uk/~zerbino/velvet/ ). There is an error when I install it.
src / readSet.c: 34:18: fatal error: zlib.h: No such file or directory
compilation terminated.
make: *** [obj / readSet.o] Error 1

I have never seen this problem, so I went to a plain Ubuntu 12 computer, and downloaded http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.07.tgz . When I typed "make" I got the same error as you.

Velvet actually comes bundled with its own copy of zlib (it is used to handle .gz compressed files). HOWEVER, it does not use it by default anymore (it used to).

To compile it with the bundled zlib, just type "make BUNDLEDZLIB=1" instead of just "make" and everything should work.

If you want to enable a larger k-mer size too, type "make BUNDLEDZLIB=1 MAXKMERLENGTH=127".

Hope this helps!

[Torst]

You need to install zlib-devel (or whatever the equivalent on your server distribution is).

I think that is correct for Redhat/Fedora/Centos:

% sudo yum install zlib-devel

For Ubuntu/Debian, you need to install zlib1g-dev:

% sudo apt-get install zlib1g-dev

If you do the above, then "make" should succeed. Otherwise just type "make BUNDLEDZLIB=1".

[Biomicrogen]

still an issue

So I tried to use the BUNDLEDZLIB=1 compile option and It did compile. That being said the veleth and velvetg application files did appear in the velvet directory, but when I tried to run them (from the velvet directory) the command was not found. Any ideas?

[DZhang]

Biomicrogen,

How did you run velveth/g? Try put ./ in front of velveth/g.

Best regards,
Douglas

https://www.contigexpress.com

[shrujan]

velvetg and velveth errors

Hi,

So I too tried to use the BUNDLEDZLIB=1 compile option and It did compile. That being said the veleth and velvetg application files did appear in the velvet directory, but when I tried to run them (from the velvet directory) the command was not found.

when i gave a velvetg or vveth 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.