Question: Errors While Running Repeatmasker
0
gravatar for tzcoolman
7.9 years ago by
tzcoolman0
tzcoolman0 wrote:

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
/*---------------------------------------------------------------*/
repeatmasker • 4.1k views
ADD COMMENTlink modified 4.8 years ago by amoltej90 • written 7.9 years ago by tzcoolman0

please, take a few seconds to format your question.

ADD REPLYlink written 7.9 years ago by Pierre Lindenbaum131k

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

 RepeatMasker -low file.fasta
ADD REPLYlink modified 7.9 years ago • written 7.9 years ago by JC11k

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?

ADD REPLYlink written 7.9 years ago by tzcoolman0

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.

ADD REPLYlink written 7.9 years ago by tzcoolman0

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

ADD REPLYlink written 7.9 years ago by GAO Yang250
0
gravatar for amoltej
4.8 years ago by
amoltej90
Australia
amoltej90 wrote:
Hey, did you find solution for your problem? I am facing same problem with error 137. Any help would be greatly appreciated. Thank you
ADD COMMENTlink written 4.8 years ago by amoltej90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1497 users visited in the last hour