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Old 06-09-2011, 10:59 PM   #1
ECHo
Member
 
Location: Taiwan

Join Date: Jan 2010
Posts: 17
Default Euler 2.0

I've tried to use EULER 2.0 to do the de novo assembly process.
However, there are error messages:
sh: line 1: 20961 Segmentation fault /home/echo/denovo/euler2_linux/trans_qual -i test.fasta -o test.fasta.reads -H >> test.fasta.log
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.txt': No such file or directory
mv: cannot stat `reads.txt.score': No such file or directory
mv: cannot stat `reads.aln': No such file or directory
rm: cannot remove `G_*.gvz': No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_et: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_db: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory


I have no idea why the messages would appear.
Does anybody know the reason and how could I solve the problem?
Thanks a lot.
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Old 06-10-2011, 07:22 PM   #2
seb567
Senior Member
 
Location: Québec, Canada

Join Date: Jul 2008
Posts: 260
Default

Quote:
Originally Posted by ECHo View Post
I've tried to use EULER 2.0 to do the de novo assembly process.
However, there are error messages:
sh: line 1: 20961 Segmentation fault /home/echo/denovo/euler2_linux/trans_qual -i test.fasta -o test.fasta.reads -H >> test.fasta.log
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.tmp': No such file or directory
mv: cannot stat `reads.tmp.score': No such file or directory
mv: cannot stat `reads.txt': No such file or directory
mv: cannot stat `reads.txt.score': No such file or directory
mv: cannot stat `reads.aln': No such file or directory
rm: cannot remove `G_*.gvz': No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_et: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_db: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory
sh: /home/echo/denovo/euler2_linux/euler_cons: /usr/libexec/ld-elf.so.1: bad ELF interpreter: No such file or directory


I have no idea why the messages would appear.
Does anybody know the reason and how could I solve the problem?
Thanks a lot.
"A segmentation fault (often shortened to segfault) or bus error is generally an attempt to access memory that the CPU cannot physically address."

--Wikipedia

It means that there is at least one programming error in the source code of EULER 2.0.

The usual way to fix that is to

1. Run the code inside gdb
2. Locate the bug and fix it
3. ???
4. Profit.

For your information, you are not alone: euler-sr problems [http://seqanswers.com]
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