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rmhubley / RepeatMasker

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
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Bus error (core dumped)/WARNING: Comparison failed. Retrying with larger minmatch (9)/sh: line 1: 8350 Killed #219

Open minhasbushra opened 1 year ago

minhasbushra commented 1 year ago

Hi,

I installed the latest version of repeat masker along with rmblast 2.14. The older version worked perfect with this file. I have Dfam3.7+ Repbase. I am getting these errors

Checking for E. coli insertion elements identifying matches to teleostei sequences in batch 59 of 17027

Checking for E. coli insertion elements identifying matches to teleostei sequences in batch 60 of 17027 sh: line 1: 18390 Bus error (core dumped) /projects//local/opt/RepeatModeler-2.0.4/rmblast-2.14.0/bin/rmblastn -num_alignments 9999999 -db /projects//local/opt/RepeatM asker-4.1.5/RepeatMasker/Libraries/CONS-Dfam_withRBRM_3.7/teleostei/specieslib -query /projects//TE/RepeatMasker/RM_30742.ThuJun10825372023/.v3.fa_batch-60.mask ed -gapopen 24 -gapextend 6 -mask_level 101 -complexity_adjust -word_size 8 -xdrop_ungap 450 -xdrop_gap_final 225 -xdrop_gap 112 -min_raw_gapped_score 225 -dust no -outfmt="6 score perc_sub percquery gap perc_db_gap qseqid qstart qend qlen sstrand sseqid sstart send slen kdiv cpg_kdiv transi transv cpg_sites qseq sseq" -num_threads 4 -matrix 20p41g.matrix 2> /projects/****/TE/RepeatMasker/RM_30742.ThuJun10825372023/ncResults-1685636993-18381-3254.77533204079.err

WARNING: Comparison failed. Retrying with larger minmatch (9) WARNING: Comparison failed. Retrying with larger minmatch (9) WARNING: Comparison failed. Retrying with larger minmatch (9) A concise description of the bug, including any error messages.

sh: line 1: 18872 Killed /projects//local/opt/RepeatModeler-2.0.4/rmblast-2.14.0/bin/rmblastn -num_alignments 9999999 -db /projects//local/opt/RepeatMasker-4.1.5/RepeatMasker/Libraries/CONS-Dfam_withRBRM_3.7/teleostei/specieslib -query /projects//TE/RepeatMasker/RM_30742.ThuJun10825372023/.v3.fa_batch-10.masked -gapopen 24 -gapextend 6 -mask_level 101 -complexity_adjust -word_size 10 -xdrop_ungap 450 -xdrop_gap_final 225 -xdrop_gap 112 -min_raw_gapped_score 225 -dust no -outfmt="6 score perc_sub perc_query_gap perc_db_gap qseqid qstart qend qlen sstrand sseqid sstart send slen kdiv cpg_kdiv transi transv cpg_sites qseq sseq" -num_threads 4 -matrix 20p43g.matrix 2> /projects/****/TE/RepeatMasker/RM_30742.ThuJun10825372023/ncResults-1685637191-8114-3607.9926653608.err

ncResults-1685634683-13832-2648.33295763069.err file says "Command line argument error: Argument "query". File is not accessible: `/projects/*/TE/RepeatMasker/RM_30742.ThuJun10825372023/**.v3.fa_batch-38.masked' "

I have reinstalled/ reconfigured but nothing seem to work.

rmhubley commented 11 months ago

Are you still having this issue? If so, could you send me some more details: what type of system are you running on, how much memory (RAM) does it have, is this a shared system, and finally can you reproduce this problem (e.g each time you run this you get an error on batch 60)?

rissidaniel commented 4 months ago

Hello, I am already having this error in the configuration of the tool: Could you please help solve it?

Add a Search Engine:

  1. Crossmatch: [ Un-configured ]

  2. RMBlast: [ Un-configured ]

  3. HMMER3.1 & DFAM: [ Configured, Default ]

  4. ABBlast: [ Un-configured ]

  5. Done

Enter Selection: 5 Building FASTA version of RepeatMasker.lib ......................... Building RMBlast frozen libraries.. sh: line 1: 3831326 Bus error (core dumped) /home/dar21/miniconda3/envs/repeat/bin//makeblastdb -dbtype nucl -in /home/dar21/miniconda3/envs/repeat/share/RepeatMasker/Libraries/RepeatMasker.lib > /dev/null 2>&1 sh: line 1: 3831492 Bus error (core dumped) /home/dar21/miniconda3/envs/repeat/bin//makeblastdb -dbtype prot -in /home/dar21/miniconda3/envs/repeat/share/RepeatMasker/Libraries/RepeatPeps.lib > /dev/null 2>&1 The program is installed with a the following repeat libraries: File: /mnt/beegfs/mnt/work/bioinfo/home/dar21/miniconda3/envs/repeat/share/RepeatMasker/Libraries/Dfam.h5 FamDB Generator: famdb.py v0.4.2 FamDB Format Version: 0.5 FamDB Creation Date: 2023-01-08 10:42:05.645898

Database: Dfam Version: 3.7 Date: 2023-01-11

Dfam - A database of transposable element (TE) sequence alignments and HMMs.

Total consensus sequences: 19768 Total HMMs: 19730

netwon123 commented 2 months ago

Hi, could you solved this error?