[rmaexpress_help] Re: RMAExpress still crashes after 1.0 beta 8

  • From: Alex Feltus <yaqona2@xxxxxxxxx>
  • To: rmaexpress_help@xxxxxxxxxxxxx
  • Date: Wed, 5 Mar 2008 06:22:27 -0800 (PST)

Is there any specificity to the corruption?  Can I
prescreen files in some way?

Alex

--- Ben Bolstad <bmb@xxxxxxxxxxxxx> wrote:

> I am guessing that there are further corrupted CEL
> files in that
> dataset. I did not have the energy to further
> examine that possibility
> yesterday.
> 
> Ben
> 
> 
> On Wed, 2008-03-05 at 06:03 -0800, Alex Feltus
> wrote:
> > Ben:
> > 
> > Thanks for your help with this.  I removed those
> two
> > .CEL files which allowed me to get to the BA stage
> > (further than before).  However, I still get a
> > segmentation fault.  
> > 
> > Alex
> > 
> > Here is the gdb output (appears to break as
> before):
> > 
> > Starting program: /usr/local/bin/RMAExpress 
> > [Thread debugging using libthread_db enabled]
> > [New Thread 47990231476192 (LWP 8626)]
> > [New Thread 1082132816 (LWP 24051)]
> > [New Thread 1090525520 (LWP 24052)]
> > [Thread 1090525520 (LWP 24052) exited]
> > [Thread 1082132816 (LWP 24051) exited]
> > [New Thread 1082132816 (LWP 24053)]
> > [New Thread 1090525520 (LWP 24054)]
> > [New Thread 1098918224 (LWP 24055)]
> > [Thread 1090525520 (LWP 24054) exited]
> > [Thread 1098918224 (LWP 24055) exited]
> > [Thread 1082132816 (LWP 24053) exited]
> > [New Thread 1082132816 (LWP 24056)]
> > [New Thread 1098918224 (LWP 24057)]
> > [Thread 1098918224 (LWP 24057) exited]
> > [Thread 1082132816 (LWP 24056) exited]
> > 
> > Program received signal SIGSEGV, Segmentation
> fault.
> > [Switching to Thread 47990231476192 (LWP 8626)]
> > 0x0000000000427480 in max_density (z=0x378a8440,
> > rows=0, cols=<value optimized out>, column=0) at
> > Preprocess/rma_background3.c:301
> > 301         if (dens_y[i] == max_y)
> > 
> > --- Ben Bolstad <bmb@xxxxxxxxxxxxx> wrote:
> > 
> > > I have investigated this issue further by first
> > > downloading all
> > > available ATH1 arrays (GPL198) from GEO. I can
> > > duplicate this error, but
> > > it is not due to a dataset size problem. Instead
> it
> > > is because one of
> > > CEL files is corrupted (GSM260954.cel for the
> > > record). There is actually
> > > also another file in that set that is corrupted,
> at
> > > least at my end
> > > (GSM226522_S17_3.CEL) though the corruption mode
> is
> > > different. Fixes for
> > > detecting these corruption types during the
> parsing
> > > face are imminent
> > > for the next beta release. I'm not sure the
> timing
> > > on this next beta,
> > > though it will probably be within the next
> couple of
> > > weeks.
> > > 
> > > I don't expect these situations to be
> particularly
> > > common so I don't
> > > believe that 1.0 beta 8 is critically damaged,
> and
> > > it is still a
> > > definite improvement over 1.0 beta 7 and earlier
> > > versions for (super)
> > > large datasets.
> > > 
> > > Best,
> > > 
> > > Ben 
> > > 
> > > 
> > > On Mon, 2008-03-03 at 10:04 -0800, Alex Feltus
> > > wrote:
> > > > Ben:
> > > > 
> > > > I can RMA 31 arrays of this type no problem,
> so
> > > the
> > > > data is good.  I have ~300GB of disk space
> that
> > > can be
> > > > used for temp files.  I also never even hit
> swap
> > > since
> > > > I have 16GB RAM.  I am using the default
> buffer
> > > > settings: 150 arrays/50,000 probe sets.
> > > > 
> > > > Here is GDB output for 460 GPL198 arrays:
> > > > 
> > > > GNU gdb 6.6-debian
> > > > Copyright (C) 2006 Free Software Foundation,
> Inc.
> > > > GDB is free software, covered by the GNU
> General
> > > > Public License, and you are
> > > > welcome to change it and/or distribute copies
> of
> > > it
> > > > under certain conditions.
> > > > Type "show copying" to see the conditions.
> > > > There is absolutely no warranty for GDB.  Type
> > > "show
> > > > warranty" for details.
> > > > This GDB was configured as
> "x86_64-linux-gnu"...
> > > > Using host libthread_db library
> > > > "/lib/libthread_db.so.1".
> > > > (gdb) R
> > > > Starting program: /usr/local/bin/RMAExpress 
> > > > [Thread debugging using libthread_db enabled]
> > > > [New Thread 47608618407904 (LWP 16114)]
> > > > [New Thread 1082132816 (LWP 16117)]
> > > > [New Thread 1090525520 (LWP 16118)]
> > > > [Thread 1090525520 (LWP 16118) exited]
> > > > [Thread 1082132816 (LWP 16117) exited]
> > > > [New Thread 1082132816 (LWP 16119)]
> > > > [New Thread 1090525520 (LWP 16120)]
> > > > [Thread 1090525520 (LWP 16120) exited]
> > > > [Thread 1082132816 (LWP 16119) exited]
> > > > [New Thread 1082132816 (LWP 16121)]
> > > > [New Thread 1090525520 (LWP 16122)]
> > > > [Thread 1090525520 (LWP 16122) exited]
> > > > [Thread 1082132816 (LWP 16121) exited]
> > > > 
> > > > Program received signal SIGSEGV, Segmentation
> > > fault.
> > > > [Switching to Thread 47608618407904 (LWP
> 16114)]
> > > > 0x0000000000427480 in max_density
> (z=0x3767c660,
> > > > rows=0, cols=<value optimized out>, column=0)
> at
> > > > Preprocess/rma_background3.c:301
> > > > 301         if (dens_y[i] == max_y)
> > > > 
> > > > 
> > > > Alex
> > > > 
> > > > 
> > > > --- Ben Bolstad <bmb@xxxxxxxxxxxxx> wrote:
> > > > 
> > > > > At least for the one dataset of this type,
> that
> > > I
> > > > > currently have
> > > > > accessible, consisting of only 24 arrays
> every
> > > thing
> > > > > processes fine with
> > > > > out complaint or crashing.
> > > > > 
> > > > > What values are you using in your Buffer
> > > settings?
> > > > > Do you have ample
> > > > > disk space in the location you are trying to
> use
> > > for
> > > > > your temporary
> > > > > space?
> > > > > 
> > > > > Ben
> > > > > 
> > > > > 
> > > > > 
> > > > > On Mon, 2008-03-03 at 07:53 -0800, Ben
> Bolstad
> > > > > wrote:
> > > > > > Ok, that makes more sense since the first
> one
> > > you
> > > > > gave me did not seem
> > > > > > to be an Affymetrix array type. I know
> that
> > > things
> > > > > worked with
> > > > > > Arabidopsis ATH1 Arrays in the past,
> though I
> > > have
> > > > > not tested with this
> 
=== message truncated ===


--
Alex Feltus, Ph.D.
Assistant Professor
Clemson University
Department of Genetics & Biochemistry
Biosystems Research Complex Rm 302C
51 New Cherry Street
Clemson, SC 29634
864-656-3231 (office) - (864) 656-6879 (fax)
http://www.clemson.edu/genbiochem/faculty/afeltus.html


      
____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  
http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 


Other related posts: