Question: RepeatMasker: createLib() Error
0
gravatar for linda
4.2 years ago by
linda0
linda0 wrote:

Hey,

I tried to install RepeatMasker in my VM Virtual Box, because i had problems with perl using windows, but still i'm struggling.

The error seems to be similar to others i have already seen, but i tried the mentioned hints.

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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.

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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

repeatmasker createlib() • 1.6k views
ADD COMMENTlink modified 4.2 years ago by _r_am32k • written 4.2 years ago by linda0

As an aside, you will never (well, almost never) need to create a link using sudo.

ADD REPLYlink written 4.2 years ago by _r_am32k

well, the link is being created in the /lib directory, so I think you need root privilege for that!

ADD REPLYlink written 4.1 years ago by arnstrm1.8k

No, the link is being created to a file in /lib/. I am pretty sure you don't need root privileges for that. AFAIK you can link to anything no matter the privilege you have on it, you just can't do stuff with the link, like read the actual file without appropriate permissions.

ADD REPLYlink modified 4.1 years ago • written 4.1 years ago by _r_am32k
2

Actually, ln -s <source> <target>. So the user is writing a shortcut to a directory under lib. You can't do that without sudo!

ADD REPLYlink written 4.1 years ago by arnstrm1.8k

Ah I see that now. Thank you!

ADD REPLYlink written 4.1 years ago by _r_am32k

@linda: Are you running 32-bit or 64-bit OS? What does uname -a report?

ADD REPLYlink written 4.2 years ago by GenoMax95k

I'm running 64 bit OS. The '-a' is the 'alignment' option, its the type of output RepeatMasker creates.

Thanks for your comments!

ADD REPLYlink written 4.2 years ago by linda0

uname is a command that reports certain information about the OS and -a is an option for that command. This has nothing to do with RepeatMasker.

ADD REPLYlink written 4.2 years ago by GenoMax95k

Not related to solving the error you are receiving..

It seemed from the input file specified in your cmd, that its a genomic fasta file. In that case, for many model organisms the location of repeats is available from RepM site as well as UCSC Table Browser.

ADD REPLYlink written 4.2 years ago by Amitm2.1k

Masked (hard and soft) chromosome files are also available from UCSC's FTP site.

ADD REPLYlink written 4.2 years ago by GenoMax95k
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