Error Invoking Makeblastdb

Question

[Naveen]

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

[Naveen]

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.

[Michael Schubert]

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

[Michael Schubert]

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

[wayma]

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.

[Ram]

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.

[Ram]

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

[linda]

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

Maybe 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

[GenoMax]

Please create a new post/question for this.

Answer 1

[Lanmenbanban]

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 !

Answer 2

[Geparada]

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

[Don]

Many thanks! This worked beautifully.

[Jonathanjacobs]

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

[bdighera]

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

Answer 3

[Robert Hubley]

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.