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Old 04-19-2011, 09:40 AM   #1
chenhao392
Junior Member
 
Location: Tucson

Join Date: Mar 2011
Posts: 4
Default Please help: In Velvetg, maximum elements addressable with 32 bits?

Hi guys,

I was trying to assemble a maize genome with Velvet, but got stuck here for a while. Any help is appreciated.

some information about the machine:

uname -a
Linux marin 2.6.16.46-0.12-default #1 SMP Thu May 17 14:00:09 UTC 2007 ia64 ia64 ia64 GNU/Linux


gcc -v
Using built-in specs.
Target: ia64-unknown-linux-gnu
Configured with: ../gcc-4.4.0/configure --prefix=/opt/gcc/4.4.0 --with-mpfr=/opt/mpfr/2.4.1 --with-gmp=/opt/gmp/4.3.1
Thread model: posix
gcc version 4.4.0 (GCC)

about the data
pair-end fastq dataset, all in 75bp, all ~15G in *.fq.gz format



about the binaries
I compile the velvet source on this machine by:
make 'OPENMP=1' 'LONGSEQUENCES=1' 'CATEGORIES=4' 'BIGASSEMBLY=1'

and got:
file velveth
velveth: ELF 64-bit LSB executable, IA-64 (Intel 64 bit architecture), version 1 (SYSV), for GNU/Linux 2.6.4, dynamically linked (uses shared libs), for GNU/Linux 2.6.4, not stripped

velvetg:
the same.

running and error
velveth run through without error with the following command:
velveth mo17 31 -reference ZmB73_RefGen_v2.RepMasked.fasta -fastq.gz -shortPaired *gz


however, when I was trying to run velvetg with the following command, program throw out the error mentioned in the title..

velvetg mo17/ -ins_length 500 -exp_cov auto -min_contig_lgth 100 -read_trkg yes -amos_file yes -unused_reads yes

the error info:
...
...
[17914.055037] Connecting 112000000 / 217984709
[17924.646873] Connecting 57000000 / 217984709
[17939.007915] Connecting 30000000 / 217984709
[17939.361960] >>> Reached maximum elements addressable with 32 bits

my trying

I tried to recompile the source with CFLAGS= -mlp64, but got error again..

gcc -mlp64 -fopenmp -O3 -D MAXKMERLENGTH=31 -D CATEGORIES=4 -D BIGASSEMBLY -D LONGSEQUENCES -D OPENMP -c src/tightString.c -o obj/tightString.o
cc1: error: unrecognized command line option "-mlp64"
make: *** [obj/tightString.o] Error 1
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Old 05-25-2011, 01:24 PM   #2
JasonD
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Location: Colorado, USA

Join Date: May 2011
Posts: 1
Default Solution?

Hi there,

Did you ever figure out how to make this work? I'm getting the same error.

Thanks!
- Jason
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Old 05-25-2011, 02:48 PM   #3
chenhao392
Junior Member
 
Location: Tucson

Join Date: Mar 2011
Posts: 4
Default

Sorry for disappointing you, I didn't make it...
I was quite busy with other works, thus can not afford the time I might take.
I took use of SOAPdenovo instead, and got a large number of scaffolds with gaps. It seems that the coverage is not good enough, or I just did sth stupid for the data..

PS: I am a rather new player in the genome assembly arena

Chen Hao
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Old 09-22-2011, 08:39 PM   #4
huhstk
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Location: usa

Join Date: Dec 2010
Posts: 1
Default

Hey Chao,
Have you found any solution? I got the same error. From the reminder, it may be caused due to run in 32bit enviroment. But I was running at state supecomputer that should be 64 bit. So strange. If you have any update, please let me know. hzh0005@auburn.edu
Hongtao
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Old 09-23-2011, 12:59 AM   #5
sklages
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Location: Berlin, DE

Join Date: May 2008
Posts: 628
Default

You should post that on the velvet mailing list.
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