[maker-devel] Question: maker Segmentation fault (core dumped)
Carson Holt
carsonhh at gmail.com
Thu Aug 2 20:07:53 MDT 2012
Ru with the –f flag before rerunning in the same directory as your previous
error. Also collect the STDERR both with and without the -debug flag and
send it to me.
Thanks,
Carson
From: "Fan;Wen-Lang 范文郎" <alangfan at gmail.com>
Date: Thursday, 2 August, 2012 8:45 PM
To: Carson Holt <carsonhh at gmail.com>
Cc: <maker-devel at yandell-lab.org>
Subject: Re: [maker-devel] Question: maker Segmentation fault (core dumped)
Thanks Carson.
I'm using a single server with centOS6 64 bit.
============================================================================
==
STATUS MAKER 2.26
============================================================================
==
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: DISABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK
----------------------------------------------------------------------------
------------------------
I have updated/reinstalled the three modules, AnyDBM_File, DBD::SQLite and
BerkeleyDB. And fix these file mentioned by Felix.
"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' *)"
I get new error messages when I run maker2.26.
==========================================================
...........
...........
Process::MpiTiers::__ANON__('Error::Simple=HASH(0x476f690)',
'SCALAR(0x284f2c0)') called at
/home/alang/tools/maker/maker/bin/../lib/Error.pm line 339
eval {...} called at
/home/alang/tools/maker/maker/bin/../lib/Error.pm line 329
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
Error::subs::try('CODE(0x476feb8)', 'HASH(0x476bc98)') called at
/home/alang/tools/maker/maker/bin/../lib/Process/MpiTiers.pm line 79
Process::MpiTiers::_prepare('Process::MpiTiers=HASH(0x476c4f0)')
called at /home/alang/tools/maker/maker/bin/../lib/Process/MpiTiers.pm line
56
Process::MpiTiers::new('Process::MpiTiers', 'HASH(0x4773be8)', 0,
'Process::MpiChunk') calledERROR: Failed while processing contig output
ERROR: Can not load chunks
WARNING: You must always set a rank before running MpiTiers
FATAL: argument `the_void` does not exist in MpiTier object
===========================================================
2012/8/2 Carson Holt <carsonhh at gmail.com>
> 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/RepeatMaske
> r #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
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/mak
> er-devel_yandell-lab.org
--
Alang
-----
范文郎
Wen-Lang Fan,
Post-doctoral Fellow,
The Genomics Research Center, Academia Sinica. 128 Academia Road,
Section 2,Nankang, Taipei, 115, Taiwan (02) 27871246
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