Question: Problems with Repeatmasker
gravatar for ccanchaya
3.5 years ago by
ccanchaya0 wrote:

Hi everybody,

I am trying to use repeatmasker, however I have multiple warnings on some sequences so that RepeatMasker aborts the analysis. I also try to skip some, but there are many sequences that give warning messages.

Any ideas how to solve this? I have updated the repbase to the latest version corresponding to our repeatmasker version The error message is the following (below):

Any idea how to solve this?

Best regards,


Checking for E. coli insertion elements
identifying Simple Repeats in batch 2 of 6
identifying matches to eukaryota sequences in batch 2 of 6
sh: línea 1: 16742 Abortado                /opt/cesga/ncbi-rmblastn/2.2.28/intel/2016/bin/rmblastn -db /mnt/lustre/scratch/home/uvi/bg/dsp/tfg/RepeatMasker/Libraries/dc20170127-rb20170127/eukaryota/specieslib -query /mnt/lustre/scratch/home/uvi/bg/dsp/tfg/lola/rm_lola_eukaryota/fragmento914/RM_16695.TueMay91304062017/lola_partida914.fa_batch-2.masked -gapopen 24 -gapextend 6 -mask_level 101 -complexity_adjust -word_size 9 -xdrop_ungap 450 -xdrop_gap_final 225 -xdrop_gap 112 -min_raw_gapped_score 225 -dust no -num_threads 4 -matrix 20p37g.matrix 2> /mnt/lustre/scratch/home/uvi/bg/dsp/tfg/lola/rm_lola_eukaryota/fragmento914/RM_16695.TueMay91304062017/ncResults-1494327891-16732.err
WARNING: Comparison failed. Retrying with larger minmatch (10)
sh: línea 1: 16775 Abortado

repeatmasker software error • 1.4k views
ADD COMMENTlink modified 23 months ago by transposable.element0 • written 3.5 years ago by ccanchaya0
gravatar for transposable.element
23 months ago by
transposable.element0 wrote:

Is There anybody could answer this question? I meet the same problem.

ADD COMMENTlink written 23 months ago by transposable.element0

I found the solution. When run RepeatMasker with cross_match as search engine, if you meet such problem, please decrease the fragment size, for example, use a parameter such as -frag 10000. Then everything will be just fine! Good luck with anybody!


ADD REPLYlink written 22 months ago by transposable.element0
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