RepeatMasker: createLib() Error
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7.5 years ago
linda • 0

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.

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

RepeatMasker • 3.5k views
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As an aside, you will never (well, almost never) need to create a link using sudo.

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

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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.

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

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Ah I see that now. Thank you!

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

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

Thanks for your comments!

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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.

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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.

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

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