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Old 06-04-2012, 12:26 PM   #1
Location: Canada, Quebec

Join Date: Apr 2012
Posts: 53
Default Consed- add454 error

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

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.

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