<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif; "><div>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.</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><span style="font-weight:bold">From: </span> "Fan;Wen-Lang 范文郎" <<a href="mailto:alangfan@gmail.com">alangfan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Thursday, 2 August, 2012 1:36 AM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] Question: maker Segmentation fault (core dumped)<br></div><div><br></div>Dear All,<br><br>I am running Maker and get "Segmentation fault (core dumped)." Below description is command line and setting.<br>Does anyone have same problem or any suggestions? <br><br>Best,<br><br>-------command and error message-------------------------------------<br>
[alang@bioinfoX temporary]$ maker -CTL<br>modify maker_opts.ctl<br>...........<br>[alang@bioinfoX temporary]$ maker <br>STATUS: Parsing control files...<br>STATUS: Processing and indexing input FASTA files...<br>Segmentation fault (core dumped)<br>
===========================================<br clear="all"><br>------- maker_opts.ctl -------------------------------------<br>#-----Genome<br>genome=/home/alang/tools/maker/maker/temporary/dpp_contig.fasta<br>#-----EST Evidence<br>
est=/home/alang/tools/maker/maker/temporary/dpp_est.fasta<br>#altest=/fastas/alt_est.fasta<br><br>#-----Protein Homology Evidence<br>#protein=protein.fasta<br><br>#-----MAKER Specific Options<br>evaluate=0<br>max_dna_len=100000<br>
min_contig=1<br>min_protein=0<br>split_hit=10000<br>pred_flank=200<br>single_exon=0<br>single_length=250<br>keep_preds=0<br>map_forward=0<br>retry=1<br>clean_try=0<br>clean_up=0<br>============================================<br><br>----------maker_exe.ctl---------------------------------------------<br>#-----Location of Executables Used by MAKER/EVALUATOR<br>makeblastdb=/home/alang/tools/maker/maker/bin/../exe/blast/bin/makeblastdb #location of NCBI+ makeblastdb executable<br>
blastn=/home/alang/tools/maker/maker/bin/../exe/blast/bin/blastn #location of NCBI+ blastn executable<br>blastx=/home/alang/tools/maker/maker/bin/../exe/blast/bin/blastx #location of NCBI+ blastx executable<br>tblastx=/home/alang/tools/maker/maker/bin/../exe/blast/bin/tblastx #location of NCBI+ tblastx executable<br>
formatdb= #location of NCBI formatdb executable<br>blastall= #location of NCBI blastall executable<br>xdformat= #location of WUBLAST xdformat executable<br>blasta= #location of WUBLAST blasta executable<br>RepeatMasker=/home/alang/tools/maker/maker/bin/../exe/RepeatMasker/RepeatMasker #location of RepeatMasker executable<br>
exonerate=/home/alang/tools/maker/maker/bin/../exe/exonerate/bin/exonerate #location of exonerate executable<br><br>#-----Ab-initio Gene Prediction Algorithms<br>snap=/home/alang/tools/maker/maker/bin/../exe/snap/snap #location of snap executable<br>
gmhmme3=/home/alang/software/gm_es_bp_linux64_v2.3e/gmes/gmhmme3 #location of eukaryotic genemark executable<br>gmhmmp= #location of prokaryotic genemark executable<br>augustus=/home/alang/tools/maker/maker/bin/../exe/augustus/bin/augustus #location of augustus executable<br>
fgenesh= #location of fgenesh executable<br><br>#-----Other Algorithms<br>probuild=/home/alang/software/gm_es_bp_linux64_v2.3e/gmes/probuild #location of probuild executable (required for genemark)<br><br>============================================<br><br>-- <br> <span style="color:rgb(102,102,102)">Alang</span><br><br>
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