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  • parulvk
    Member
    • Oct 2011
    • 12

    #1

    RepeatMasker error

    I am using RepeatMasker with custom library of sequences to be masked in
    the query. Here is the command that I have been using:
    ------------------------------------
    # ./RepeatMasker -q -no_is -nolow -lib repeats.fasta genome.fa
    ------------------------------------
    here is the output along with error:
    identifying matches to Lv-repeats.fasta sequences in batch 53 of 11907
    WARNING: The search engine returned an error (141)
    A search phase could not complete on this batch.
    The batch file will be re-run and if possible the
    program will resume.
    WARNING: Retrying batch ( 53 )...
    identifying matches to Lv-repeats.fasta sequences in batch 53 of 11907
    WARNING: The search engine returned an error (141)
    A search phase could not complete on this batch.
    The batch file will be re-run and if possible the
    program will resume.
    WARNING: Retrying batch ( 53 )...
    identifying matches to Lv-repeats.fasta sequences in batch 53 of 11907
    WARNING: The search engine returned an error (141)
    A search phase could not complete on this batch.
    The batch file will be re-run and if possible the
    program will resume.
    FATAL ERROR: RepeatMasker giving up. One or more
    batches failed! Unfortunately this type of error
    cannot be recovered from. Please submit this output
    to the feedback page at the repeatmasker website:

    Further details about this problem may be found in
    the directory:
    /RepeatMasker/RM_5858.WedOct261410592011
    --------------------------

    The RM_5858.WedOct261410592011 directory consists of empty log file and does
    not have any clues about the error.

    Please advice how this error could be resolved.

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