Errors While Running Repeatmasker

Question

[tzcoolman]

I tried to run RepeatMasker to remove low complexity reads from my query data GC_40_2W.fa But sadly, I got error msg which indicates that rmblastn didnt process the query correctly.

Does anyone know anything about this?

Thanks in advance Enze

/*---------------------------------------------------------------*/
RepeatMasker version open-3.3.0
Master RepeatMasker Database: /bubo/home/h16/enze/RepeatMasker/Libraries/RepeatMaskerLib.embl ( Complete Database: 20120418 )



analyzing file GC_40_2W.fa

Checking for E. coli insertion elements
sh: line 1:  3132 Aborted                 (core dumped) /bubo/home/h16/enze/rmblast-1.2-ncbi-blast-2.2.23+-src/bin/rmblastn -db /bubo/home/h16/enze/RepeatMasker/Libraries/20120418/general/is.lib -query /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/GC_40_2W.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix 2> /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/ncResults-1355412092.err
WARNING: The search engine returned an error (134)
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 ( 1 )...

Checking for E. coli insertion elements
sh: line 1:  3217 Aborted                 (core dumped) /bubo/home/h16/enze/rmblast-1.2-ncbi-blast-2.2.23+-src/bin/rmblastn -db /bubo/home/h16/enze/RepeatMasker/Libraries/20120418/general/is.lib -query /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/GC_40_2W.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix 2> /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/ncResults-1355412095.err
WARNING: The search engine returned an error (134)
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 ( 1 )...

Checking for E. coli insertion elements
sh: line 1:  3221 Aborted                 (core dumped) /bubo/home/h16/enze/rmblast-1.2-ncbi-blast-2.2.23+-src/bin/rmblastn -db /bubo/home/h16/enze/RepeatMasker/Libraries/20120418/general/is.lib -query /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/GC_40_2W.fa_batch-1.masked -gapopen 12 -gapextend 2 -complexity_adjust -word_size 15 -xdrop_ungap 34 -xdrop_gap_final 17 -xdrop_gap 8 -min_raw_gapped_score 17 -dust no -num_threads 4 -matrix identity.matrix 2> /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012/ncResults-1355412098.err
WARNING: The search engine returned an error (134)
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: /bubo/home/h16/enze/RepeatMasker/RM_3123.ThuDec131620572012
/*---------------------------------------------------------------*/

[Pierre Lindenbaum]

please, take a few seconds to format your question.

[JC]

what command did you use? In general I use for masking low complexity regions:

 RepeatMasker -low file.fasta

[tzcoolman]

I simply use RepeatMasker test.fasta and get failed. 90% that the problem comes from incorrect installation. Could u be kind and tell me how do u install rmblastn?

[tzcoolman]

RepeatMasker test.fasta. That's what I used. Could u tell me how did u install rmblastn. I suspect that the problem might come from there.

[JC]

http://repeatmasker.org/RMDownload.html http://www.repeatmasker.org/RMBlast.html

[GAO Yang]

Has it ran successfully before? Maybe it's the problem with the installation, I think.

Answer 1

[amoltej]

Hey, did you find solution for your problem? I am facing same problem with error 137. Any help would be greatly appreciated. Thank you