[maker-devel] MAKER2.23 output

[Carson Holt]

Segmentation fault means there was a failure with C code.  It was likely in
one of the modules being used.

These are all potential culprits

Inline::C
Proc::ProcessTable
DB_file
forks

Based on when the error occurred.  I would lean more toward DB_File.  Is it
possible that BerkleyDB has been updated on your system, perhaps as part of
another installation or a system update?  That sometimes breaks this module
(which is part of the perl core).

You can try reinstalling that module from CPAN.  Also if you run MAKER
version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug')
to get more information just before the error occurs.  You can then capture
the error log send that to me.

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tue, 17 Apr 2012 16:46:40 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER2.23 output

Hi, 

I tried running the latest version of Maker 2.23 with my dataset but with
out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output
files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2
/usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further
details

I was able run the previous version of Maker 2.10 successfully with my
dataset.

Thanks,
Ranjani


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