[maker-devel] Question: maker Segmentation fault (core dumped)

[Carson Holt]

The timing of the fault suggests either a problem with your AnyDBM_File
module, BDB::SQLlite module, or BerkeleyDB module.  Could you run maker
--debug and send me the output as well as your version of maker?  Also try
updating those 3 modules on your system.

Thanks,
Carson



From:  "Fan;Wen-Lang 范文郎" <alangfan at gmail.com>
Date:  Thursday, 2 August, 2012 1:36 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Question: maker Segmentation fault (core dumped)

Dear All,

I am running Maker and get "Segmentation fault (core dumped)."  Below
description is command line and setting.
Does anyone have same problem or any suggestions?

Best,

-------command and error message-------------------------------------
 [alang at bioinfoX temporary]$ maker -CTL
modify maker_opts.ctl
...........
[alang at bioinfoX temporary]$ maker
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
Segmentation fault (core dumped)
===========================================

------- maker_opts.ctl -------------------------------------
#-----Genome
genome=/home/alang/tools/maker/maker/temporary/dpp_contig.fasta
#-----EST Evidence
est=/home/alang/tools/maker/maker/temporary/dpp_est.fasta
#altest=/fastas/alt_est.fasta

#-----Protein Homology Evidence
#protein=protein.fasta

#-----MAKER Specific Options
evaluate=0
max_dna_len=100000
min_contig=1
min_protein=0
split_hit=10000
pred_flank=200
single_exon=0
single_length=250
keep_preds=0
map_forward=0
retry=1
clean_try=0
clean_up=0
============================================

----------maker_exe.ctl---------------------------------------------
#-----Location of Executables Used by MAKER/EVALUATOR
makeblastdb=/home/alang/tools/maker/maker/bin/../exe/blast/bin/makeblastdb
#location of NCBI+ makeblastdb executable
blastn=/home/alang/tools/maker/maker/bin/../exe/blast/bin/blastn #location
of NCBI+ blastn executable
blastx=/home/alang/tools/maker/maker/bin/../exe/blast/bin/blastx #location
of NCBI+ blastx executable
tblastx=/home/alang/tools/maker/maker/bin/../exe/blast/bin/tblastx #location
of NCBI+ tblastx executable
formatdb= #location of NCBI formatdb executable
blastall= #location of NCBI blastall executable
xdformat= #location of WUBLAST xdformat executable
blasta= #location of WUBLAST blasta executable
RepeatMasker=/home/alang/tools/maker/maker/bin/../exe/RepeatMasker/RepeatMas
ker #location of RepeatMasker executable
exonerate=/home/alang/tools/maker/maker/bin/../exe/exonerate/bin/exonerate
#location of exonerate executable

#-----Ab-initio Gene Prediction Algorithms
snap=/home/alang/tools/maker/maker/bin/../exe/snap/snap #location of snap
executable
gmhmme3=/home/alang/software/gm_es_bp_linux64_v2.3e/gmes/gmhmme3 #location
of eukaryotic genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/home/alang/tools/maker/maker/bin/../exe/augustus/bin/augustus
#location of augustus executable
fgenesh= #location of fgenesh executable

#-----Other Algorithms
probuild=/home/alang/software/gm_es_bp_linux64_v2.3e/gmes/probuild #location
of probuild executable (required for genemark)

============================================

-- 
      Alang

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