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  • tnguyen
    replied
    Hi Rahul,

    How large was your genome? How much memory was needed for your run? I received this error message at the start of Step 2:

    "Could not allocate space for sequence"
    Last edited by tnguyen; 09-22-2012, 07:01 AM.

    Leave a comment:


  • rahularjun86
    replied
    Dear All,
    I ran Repeatscout successfully, Commands I used:
    Code:
    1225 ##RepeatSout Run
    1226 #step1
    1227 build_lmer_table -l 14 -sequence Final_assembly.fasta -freq Final_assembly.freq
    1228 #step2
    1229 RepeatScout -sequence Final_assembly.fasta -output Final_assembly_repeats.fasta -freq Final_assembly.freq -l 14
    1230 #step3
    1231 cat Final_assemblyf_repeats.fasta | filter-stage-1.prl > Final_assembly_repeats_filtered_stg1.fasta
    1232 #step4
    1233 RepeatMasker -pa 20 -s -lib Final_assembly_repeats_filtered_stg1.fasta Final_assembly.fasta &
    1234 #step5
    1235 cat Final_assembly_repeats_filtered_stg1.fasta | filter-stage-2.prl --cat=Final_assembly.fasta.out --thresh=3 > Final_assembly_repeats_filtered_stg2_thresh3.fasta
    1236 #step6
    1237 RepeatMasker -pa 20 -s -lib Final_assembly_repeats_filtered_stg2_thresh3.fasta Final_assembly.fasta &

    Leave a comment:


  • WhatsOEver
    replied
    Thats true and it works fine, but RepeatModeler also uses RepeatMasker and eventually the rmblast package, so you might have to face the same problems as described before.

    Leave a comment:


  • gprakhar
    replied
    Hello,

    This is not a direct answer to your question, but there is a tool from the Repeat Masker group.
    Its called Repeat Modeler, this tool integrates Repeat Scout, RECON and TRF.
    It creates a de-novo repeat library and then annotates the sequences.
    Repeat Modeler

    --
    pg

    Leave a comment:


  • WhatsOEver
    replied
    I don't know if its still an actual problem, but I had it too and was able to solve it on my system (ubuntu11, 64bit).
    The libs RepeatMasker is looking for are not the downloaded ones, but the blast dbs that should have been created by rmblast. rmblast itself is looking for a libpcre.so.0 file which it could not find on my system. The file is known to cause problems with some progs as symlinks are not made correctly during updates.
    Therefore I just created symlinks manually in my /lib/ and /lib32/ folder to the actual file (so just type "sudo ln -s /lib/libpcre.so.3 /lib/libpcre.so.0" and "sudo ln -s /lib32/libpcre.so.3 /lib32/libpcre.so.0") and afterwards everything worked fine for me

    @edge: you don't need to change anything in the .prl file, but you need to rename the trf404-linux64 (or else) executable to simply to trf.
    Last edited by WhatsOEver; 04-20-2012, 01:27 AM.

    Leave a comment:


  • sameoldmike
    replied
    same thing happened to me -- the filtered output file is empty after running for a very long time. it was run on a repeat-rich genome.

    could it be that i don't have nseg and TRF properly installed? there is no output about those two programs that i can see...

    Leave a comment:


  • hkuntal
    replied
    repeatscout

    hello everyone
    i m try to work with repeatscout but every time when i m runninf filter-stage-1.prl, the filtered library generated is created empty( no data)..... any solution???

    Leave a comment:


  • edge
    replied
    Hi Zimbobo,

    Can I ask you how you edit the perl script, filter-stage-1.prl to allow it point to the TRF path that we install?
    Which line of filter-stage-1.prl that we need to edit the path of TRF?
    My server keep on shown the below message:
    "No such file or directory at ./filter-stage-1.prl line 110"
    Thanks a lot for your sharing and guiding.

    Leave a comment:


  • Zimbobo
    replied
    I actually followed those instructions.

    RepeatMasker is complaining still about missing libraries (ie Libraries/RepeatMasker.lib etc) and advises to get something from www.girinst.org.

    The whole point of running RepeatScout for me is to build my own library. Is there a flag to teach RepeatMasker not to look for those libraries or is there a reason RepeatMasker must have those libraries?

    Leave a comment:


  • darked89
    replied
    Here is a recipe how to install and run RepeatScout:



    Hope it helps,

    Darek

    Leave a comment:


  • Zimbobo
    started a topic RepeatMasker & RepeatScout

    RepeatMasker & RepeatScout

    Hello there,

    I was wondering whether anybody on this list could knows how to run RepeatScout (1.0.5) and RepeatMasker (3.2.8).

    Basically I have a new genome, and want to use RepeatScout to make a
    library for RepeatMasker.

    Here is what I do:

    build_lmer_table -sequence genome.fa -freq genome.fq
    RepeatScout -sequence genome.fa -output repeats.fa -freq genome.fq
    filter-stage-1.prl repeats.fa &> repeats.fa.filter_1
    RepeatMasker genome.fa -e abblast -lib repeats.fa.filter_1

    Now:
    Do I use the correct file for -lib?
    RepeatMasker is still complaining about not finding Libraries/RepeatMasker.lib
    and Libraries/RepeatmaskerLib.embl.

    Thanks a lot in advance for any help.

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