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
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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