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Old 10-26-2011, 02:59 PM   #1
parulvk
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Location: California

Join Date: Oct 2011
Posts: 12
Default 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:
www.repeatmasker.org
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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