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Old 06-04-2012, 12:26 PM   #1
Antony03
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Default Consed- add454 error

Hi! I'm trying to add 454 reads and I got an error:

Code:
antony@ubuntu:~/Desktop/CONSED/edit_dir$ add454Reads.perl HAFNleavi_AllContigs.ace SFF.fof HAFNleavi_AllContigs.fna
extracting reads from sff file ../sff_dir/HBY09XS02.default.RL2.sff...
executing: /usr/local/genome/bin/consed  -sff2PhdBall ../sff_dir/HBY09XS02.default.RL2.sff -phdBall ../phdball_dir/phd.ball.1
-sff2PhdBall will be run.
no ~/consedrc file so no user resources will be used--that's ok
no consedrc file so no project-specific resources--that's ok
couldn't open readOrder.txt--that's ok
complementing LoxP because it is not palindromic
not complementing linker because it is palindromic
extracting all reads from sff file ../sff_dir/HBY09XS02.default.RL2.sff
Now processing sff file ../sff_dir/HBY09XS02.default.RL2.sff
number_of_reads = 175771
.....couldn't execute /usr/local/genome/bin/consed  -sff2PhdBall ../sff_dir/HBY09XS02.default.RL2.sff -phdBall ../phdball_dir/phd.ball.1 at /usr/local/genome/bin/add454Reads.perl line 110, <filSffFof> line 1.
Is somebody have an idea why I get this error? I use consed 23.

Thanks!
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Old 06-04-2012, 10:52 PM   #2
sklages
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have you tested your installation as recommended in the manual?
Looks as there is no "/usr/local/genome/bin/consed" or you don't have permissions to execute it. Or you are executing a 64bit consed on a 32bit "linux" box?

Current consed releases come with an installation script. Have you used that?

Sven
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Old 06-05-2012, 05:00 AM   #3
Antony03
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Quote:
Current consed releases come with an installation script. Have you used that?
Yes I used the installation script.
Quote:
Or you are executing a 64bit consed on a 32bit "linux" box?
I'm using 64 bit ubuntu:
Code:
antony@ubuntu:~/Desktop/454_newbler/edit_dir$ uname -a
Linux ubuntu 3.2.0-23-generic #36-Ubuntu SMP Tue Apr 10 20:39:51 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux
I can run Consed when I create the repertory on other computer and transfer it on mine. The script doesn't create the phd.ball.2 in the phdball_dir...
Thanks
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Old 06-05-2012, 05:08 AM   #4
sklages
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Does "/usr/local/genome/bin/consed" exist? What happens if you run the command
manually (just to see an error):

/usr/local/genome/bin/consed -sff2PhdBall ../sff_dir/HBY09XS02.default.RL2.sff -phdBall ../phdball_dir/phd.ball.1
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Old 06-05-2012, 07:14 AM   #5
Antony03
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Yes "/usr/local/genome/bin/consed" exist.

This is what I receive when I lunch it manually:

Code:
antony@ubuntu:~/Desktop/CONSED/edit_dir$ /usr/local/genome/bin/consed -sff2PhdBall ../sff_dir/HBY09XS02.default.RL2.sff -phdBall ../phdball_dir/phd.ball.1
-sff2PhdBall will be run.
no ~/consedrc file so no user resources will be used--that's ok
no consedrc file so no project-specific resources--that's ok
couldn't open readOrder.txt--that's ok
complementing LoxP because it is not palindromic
not complementing linker because it is palindromic
extracting all reads from sff file ../sff_dir/HBY09XS02.default.RL2.sff
Now processing sff file ../sff_dir/HBY09XS02.default.RL2.sff
number_of_reads = 175771
.....Segmentation fault (core dumped)
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Old 06-05-2012, 11:21 AM   #6
sklages
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Quote:
Originally Posted by Antony03 View Post
.....Segmentation fault (core dumped)
[/CODE]
It should never segfault. There are two versions of the binary in the distribution,
one statically and one dynamically linkes executable. Which one have you used?
Try the corresponding other binary version. Does it segfault as well?

If the problem persist, you should ask David Gordon to help or post to
the consed mailing list.

Sven
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Old 06-05-2012, 05:41 PM   #7
Antony03
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Thanks Sven for your help! Consed works fine now! I downloaded again HBY09XS02.default.RL2.sff from my server and that's works! The first file was probably corrupted or anything else like that. Anyway, thanks
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