Question: Error Invoking Makeblastdb
4
gravatar for Naveen
9.5 years ago by
Naveen50
Naveen50 wrote:

I installed repeat masker and the necessary components on my system with Biolinux6.0. However when i try to run repeat masker i get the following error:

RepeatMasker version open-3.3.0
Search Engine: NCBI/RMBLAST
Master RepeatMasker Database: /home/chipseq/Naveen/repmasker/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20110419 )


Building general libraries in: /home/chipseq/Naveen/repmasker/RepeatMasker/Libraries/20110419/general
RepeatMasker::createLib(): Error invoking /home/chipseq/Naveen/repmasker/rmblast/bin/makeblastdb on file /home/chipseq/Naveen/repmasker/RepeatMasker/Libraries/20110419/general/at.lib.

Can somebody please help me with this issue.

Naveen

makeblastdb error repeatmasker • 7.0k views
ADD COMMENTlink modified 4.0 years ago by linda0 • written 9.5 years ago by Naveen50
1

Unfortunately , repeat masker is not giving me any more output than what i have posted even when i opt for their option to print the progress report of search engine.

ADD REPLYlink written 9.5 years ago by Naveen50

Is there an option to give you a little more verbose output?

ADD REPLYlink written 9.5 years ago by Michael Schubert7.0k

Have you checked if both files (makeblastdb executable and at.lib) referenced in the last line exist?

ADD REPLYlink written 9.5 years ago by Michael Schubert7.0k
7
gravatar for Lanmenbanban
9.4 years ago by
Lanmenbanban70
Lanmenbanban70 wrote:

I have the same problem.

now I got the answer.

you check your system lib whether you have the file libpcre.so.0 under the /lib.

if you miss it, the programe rmblast can't work. In recent linux, this file is replaced by libpcre.so.3 or higher version. so when you use rmblast engine, it can't work.

you can make a link to the lib libpcre.so.3 with name "libpcre.so.0". Then it works wel.

Good luck !

ADD COMMENTlink written 9.4 years ago by Lanmenbanban70
7
gravatar for Geparada
9.4 years ago by
Geparada1.4k
Cambridge
Geparada1.4k wrote:

The lanmenbanban solution works perfect!!

First of all, you have to locate the libpcre.so. files:

$ locate libpcre.so.
/lib/x86_64-linux-gnu/libpcre.so.3
/lib/x86_64-linux-gnu/libpcre.so.3.12.1
/lib32/libpcre.so.3
/lib32/libpcre.so.3.12.1

I didn't have the libpcre.so.0, but making the link...

$ rmblastn
   rmblastn: error while loading shared libraries: libpcre.so.0: cannot open shared object file: No such file or directory

$ sudo ln -s /lib/x86_64-linux-gnu/libpcre.so.3 /lib/x86_64-linux-gnu/libpcre.so.0

$ rmblastn
    BLAST query/options error: Either a BLAST database or subject sequence(s) must be specified
ADD COMMENTlink modified 9.4 years ago • written 9.4 years ago by Geparada1.4k

this gave me the answer I was looking for. Nice work.

ADD REPLYlink written 9.2 years ago by Jonathanjacobs250

I was having a similar problem trying running a standalone splign application. This completely solved my problem. Thanks!

ADD REPLYlink written 3.8 years ago by bdighera0
0
gravatar for Don
9.4 years ago by
Don20
Don20 wrote:

Many thanks! This worked beautifully.

ADD COMMENTlink written 9.4 years ago by Don20
0
gravatar for Robert Hubley
8.9 years ago by
Robert Hubley10 wrote:

This is correct. The pre-compiled versions of rmblastn were done with an older UNIX system. We don't have alot of resources to compile the program on as many machines as NCBI does so we also distribute the source for people to compile it themselves. In the future NCBI will be distributing rmblastn with the main NCBI Blast release and then there will be more choices for binary distributions.

ADD COMMENTlink written 8.9 years ago by Robert Hubley10
0
gravatar for wayma
6.3 years ago by
wayma0
Tunisia
wayma0 wrote:

Hello everybody,

I have the same problem :

RepeatMasker version open-4.0.3
Search Engine: NCBI/RMBLAST [ 2.2.27+ ]
Master RepeatMasker Database: /usr/local/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20140131 )


Building general libraries in: /usr/local/RepeatMasker/Libraries/20140131/general
RepeatMasker::createLib(): Error invoking /usr/local/rmblast/bin/makeblastdb on file /usr/local/RepeatMasker/Libraries/20140131/general/at.lib.

I made a link  and I tried to locate lipcre.so. and that's what I found:

~# locate libpcre.so.
/lib/x86_64-linux-gnu/libpcre.so.0
/lib/x86_64-linux-gnu/libpcre.so.3
/lib/x86_64-linux-gnu/libpcre.so.3.13.1

It's not the same locations that mentioned in the answer . I wonder if someone could help me or explain to me how to obtain the other locations . I made a copy of the two libpcre in/lib but the command locate don't mention the copies.

 

 

ADD COMMENTlink written 6.3 years ago by wayma0

Hi,

You can just add a symbolic link to the location you find the file in. Like so:

ln -s /lib/x86_64-linux-gnu/libpcre.so.0

Run the command above in the folder you would like to execute rmblastn in.

ADD REPLYlink written 6.3 years ago by _r_am31k

Also, it's better to start a new thread than try and resurrect a thread that has been dead for over 2.5 years :-)

ADD REPLYlink written 6.3 years ago by _r_am31k
0
gravatar for linda
4.0 years ago by
linda0
linda0 wrote:

Hey,

I have a similar problem: I tried to install RepeatMasker in my VM Virtual Box, because i had problems with perl using windows.

The error seems to be the same but i already tried the mentioned hints above.


linda@linda-VirtualBox:~/Schreibtisch/RM/RepeatMasker$ ./RepeatMasker -a HS_chr1.fasta RepeatMasker version open-4.0.6 Search Engine: NCBI/RMBLAST [ 2: /home/linda/Schreibtisch/RM/ncbi-rmblast-2.2.28/bin/rmblastn: Syntax error: word unexpected (expecting ")") ] Master RepeatMasker Database: /home/linda/Schreibtisch/RM/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20160829 )

Building general libraries in: /home/linda/Schreibtisch/RM/RepeatMasker/Libraries/20160829/general RepeatMasker::createLib(): Error invoking /home/linda/Schreibtisch/RM/ncbi-rmblast-2.2.28/bin/makeblastdb on file /home/linda/Schreibtisch/RM/RepeatMasker/Libraries/20160829/general/at.lib.


when i type: locate libpcre.so.

it says: /lib/i386-linux-gnu/libpcre.so.3 /lib/i386-linux-gnu/libpcre.so.3.13.2

i already typed: sudo ln -s /lib/i386-linux-gnu/libpcre.so.3 /lib/i386-linux-gnu/libpcre.so.0

maby the problem is that i don't have the '/lib/x86_64-linux-gnu/...'?

Does someone know what to do?

Thanks a lot!!

Greetings from Germany

ADD COMMENTlink written 4.0 years ago by linda0
1

Please create a new post/question for this.

ADD REPLYlink written 4.0 years ago by GenoMax93k
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