Thanks Carson.<br><br>I'm using a single server with centOS6 64 bit.<br>==============================================================================<br>STATUS MAKER 2.26<br>==============================================================================<br>
PERL Dependencies: VERIFIED<br>External Programs: VERIFIED<br>External C Libraries: VERIFIED<br>MPI SUPPORT: DISABLED<br>MWAS Web Interface: DISABLED<br>MAKER PACKAGE: CONFIGURATION OK<br>
----------------------------------------------------------------------------------------------------<br><br>I have updated/reinstalled the three modules, AnyDBM_File, DBD::SQLite and BerkeleyDB. And fix these file mentioned by Felix.<br>
"sed -i 's/qw(DB_File GDBM_File NDBM_File SDBM_File)/qw(DB_File)/' $(grep -l 'DB_File GDBM_File NDBM_File SDBM_File' *)"<br><br>I get new error messages when I run maker2.26.<br>==========================================================<br>
...........<br>...........<br>Process::MpiTiers::__ANON__('Error::Simple=HASH(0x476f690)', 'SCALAR(0x284f2c0)') called at /home/alang/tools/maker/maker/bin/../lib/Error.pm line 339<br> eval {...} called at /home/alang/tools/maker/maker/bin/../lib/Error.pm line 329<br>
Error::subs::run_clauses('HASH(0x476bc98)', 'ERROR: Fasta index error\x{a} at /home/alang/tools/maker/maker/bi...', undef, 'ARRAY(0x285be30)') called at /home/alang/tools/maker/maker/bin/../lib/Error.pm line 426<br>
Error::subs::try('CODE(0x476feb8)', 'HASH(0x476bc98)') called at /home/alang/tools/maker/maker/bin/../lib/Process/MpiTiers.pm line 79<br> Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x476c4f0)') called at /home/alang/tools/maker/maker/bin/../lib/Process/MpiTiers.pm line 56<br>
Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x4773be8)', 0, 'Process::MpiChunk') calledERROR: Failed while processing contig output <br>ERROR: Can not load chunks<br>WARNING: You must always set a rank before running MpiTiers<br>
FATAL: argument `the_void` does not exist in MpiTier object<br>===========================================================<br><br><div class="gmail_quote">2012/8/2 Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><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><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> "Fan;Wen-Lang S¤å¦" <<a href="mailto:alangfan@gmail.com" target="_blank">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" target="_blank">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><div class="h5"><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></div></div>
_______________________________________________
maker-devel mailing list
<a href="mailto:maker-devel@box290.bluehost.com" target="_blank">maker-devel@box290.bluehost.com</a>
<a href="http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org" target="_blank">http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org</a>
</span></div>
</blockquote></div><br><br clear="all"><br>-- <br> <span style="color:rgb(102,102,102)">Alang</span><br>-----<br>S¤å¦<br>Wen-Lang Fan,<br>Post-doctoral Fellow,<br>The Genomics Research Center, Academia Sinica. 128 Academia Road,<br>
Section 2,Nankang, Taipei, 115, Taiwan (02) 27871246 <br>----------------------------------------------------------------------------------------------------------<br>