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Old 10-19-2010, 07:21 AM   #1
AndreaB
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Default CAP3 parameters within TGICL pipeline

Hello!

I would like to alter the CAP3 assembly parameters but I would like to use it within the TGICL pipeline. The TGICL usage only explains how to alter the clustering parameters. Could somebody point me to where I can edit the parameters for CAP3? Preferably I would like to keep the pipeline setup but TGICL allows splitting the clustering from CAP3 if need be.

Thank you very much!
Andrea
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Old 10-19-2010, 07:36 AM   #2
kmcarr
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The TGICL -O option accepts a list of CAP3 options which are passed to that program. The default tgicl simply passes "-p 93" to cap3 (specifying an overlap identify of 93%). All of the CAP3 options passed from the TGICL command line should be enclosed in quotes, e.g.:

Code:
tgicl [some options] -O '-p 95 -y 250 -g 2 -o 25' [some other options] <fasta_file>
Obviously what follows -O can be any valid CAP3 options. A word of warning though, if you pass invalid CAP3 options TGICL will fail and it won't be immediately obvious why it did so. You will have to dig deeper into the error logs with the asm*/ directories.

Last edited by kmcarr; 10-19-2010 at 07:38 AM.
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Old 10-19-2010, 08:05 AM   #3
AndreaB
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Hi Kevin!

Thanks a lot for your help, this is just what I needed!

Andrea
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Old 11-04-2010, 07:03 AM   #4
Obstler
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Hello,

i used tgicl, first it works very fine but it stops during assemble step.
I copied all perl scripts an binaries plus TGI folder into my /usr/local/bin path
so the missed driver is in ???

Thank you for any help

Uwe


>>> --- Initialization [allcontigs.fa] started at Nov 4 14:19:13 2010
tgicl running options:
tgicl -F allcontigs.fa -c 3
Standard log file: tgicl_allcontigs.fa.log
Error log file: err_tgicl_allcontigs.fa.log
Using 3 CPUs for clustering and assembly
Path is : /usr/local/bin/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-= Rebuilding allcontigs.fa indices =-
211456 entries from file allcontigs.fa were indexed in file allcontigs.fa.cidx
>>> --- clustering [allcontigs.fa] started at Nov 4 14:19:18 2010
Launching distributed clustering:
psx -p 3 -n 1000 -i allcontigs.fa -d cluster -C '/home/uwe2/Desktop/Bioinformatik/allcontigs/temp3/allcontigs.fa:94:30:40:' -c '/usr/local/bin/tgicl_cluster.psx'
WAITING for all children to finish before starting last child!
WAITING for all children to finish!
<<< --- clustering [allcontigs.fa] finished at Nov 4 14:20:26 2010
Running transitive closure command: gzip -cd allcontigs.fa_cl_tabhits_*.Z | tclust PID=94 OVL=40 OVHANG=30 -o allcontigs.fa_cl_clusters

PID=94
OVHANG=30
OVL=40
Total t-clusters: 38679
Largest cluster has 1972 nodes
*** all done ***
The clusters are stored in file 'allcontigs.fa_cl_clusters'.

>>> --- ASSEMBLE [allcontigs.fa] started at Nov 4 14:20:31 2010
WAITING for all children to finish before starting last child!
WAITING for all children to finish!
Can't locate TGI/DBDrv/Driver/.pm in @INC (@INC contains: /usr/local/bin /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at (eval 10) line 2.
BEGIN failed--compilation aborted at (eval 10) line 2.

Package TGI:BDrv, File /usr/local/bin/TGI/DBDrv.pm, Line 42 == Can not load driver TGI:BDrv:river::!
[ TGI::Exception has been thrown ]

Can't locate TGI/DBDrv/Driver/.pm in @INC (@INC contains: /usr/local/bin /etc/perl /usr/local/lib/perl/5.10.0 /usr/local/share/perl/5.10.0 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at (eval 10) line 2.
BEGIN failed--compilation aborted at (eval 10) line 2.

Package TGI:BDrv, File /usr/local/bin/TGI/DBDrv.pm, Line 42 == Can not load driver TGI:BDrv:river::!
[ TGI::Exception has been thrown ]

Rethrow (TGI::Exception) : Package main, File /usr/local/bin/tgicl, Line 534 ==
cat: err_tgicl_allcontigs.fa.log: No such file or directory

Process terminated with an error, at step 'ASSEMBLE'!
tgicl (allcontigs.fa) encountered an error at step ASSEMBLE
Working directory was /home/uwe2/Desktop/Bioinformatik/allcontigs/temp3.
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Old 11-04-2010, 07:56 AM   #5
kmcarr
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Quote:
Originally Posted by Obstler View Post
I copied all perl scripts an binaries plus TGI folder into my /usr/local/bin path so the missed driver is in ???
Uwe,

The error message indicates that you are using TGICL v2.0 but your installation method only works for earlier versions. Do not follow the installation instructions in the README file; look in the WhatsNew file for instructions on installing v2.0. This will install all of the files in their proper locations. (Alternatively you could use the RPM or DEB package installations available on Sourceforge.)
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Old 11-04-2010, 09:27 AM   #6
Obstler
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Hallo Kevin

thank you for your quite fast answer.
Do i need running ./Build install as root sudo ??

lino@lino-laptop:~/Programme/TGICL-2.0$ perl Build.PL
Deleting _build
Creating custom builder _build/lib/BLD.pm in _build/lib
Checking whether your kit is complete...
Looks good

Checking prerequisites...
Looks good

Deleting Build
Removed previous script 'Build'

Creating new 'Build' script for 'TGICL' version '2.0'
lino@lino-laptop:~/Programme/TGICL-2.0$ ./Build install
Manifying blib/lib/TGI/Exception.pm -> blib/libdoc/TGI::Exception.3pm
Manifying blib/lib/TGI/DBDrv/Driver/mysql.pm -> blib/libdoc/TGI:BDrv:river::mysql.3pm
Manifying blib/lib/TGI/DBDrv/Driver/oracle.pm -> blib/libdoc/TGI:BDrv:river:racle.3pm
Manifying blib/lib/TGI/Mailer.pm -> blib/libdoc/TGI::Mailer.3pm
Manifying blib/lib/TGI/DBDrv.pm -> blib/libdoc/TGI:BDrv.3pm
Manifying blib/lib/TGI/DBDrv/Driver.pm -> blib/libdoc/TGI:BDrv:river.3pm
Manifying blib/lib/TGI/Util.pm -> blib/libdoc/TGI::Util.3pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/Util.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/Exception.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/DBDrv.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/Mailer.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/DBDrv/Driver.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/DBDrv/Driver/mysql.pm
perl -pi -e 's/#-.*$//g' blib/lib/TGI/DBDrv/Driver/oracle.pm
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
ERROR: Can't create '/usr/local/bin'
Do not have write permissions on '/usr/local/bin'
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
at /usr/share/perl/5.10/Module/Build/Base.pm line 2985
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Old 11-04-2010, 09:36 AM   #7
kmcarr
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Quote:
Originally Posted by Obstler View Post
Do i need running ./Build install as root sudo ??
Yes, you do.
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Old 11-04-2010, 10:01 AM   #8
Obstler
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May be i got now a permission problem ??
I checked the location for perl scripts and folders they are in /usr/local/bin....
the building and install process runs fine

>>> --- Initialization [contig.fa] started at Nov 4 18:53:09 2010
tgicl running options:
tgicl -F contig.fa -O -p 70 -y 15 -s 251 -o 18 -i 31 -j 31
Standard log file: tgicl_contig.fa.log
Error log file: err_tgicl_contig.fa.log
Using 1 CPUs for clustering and assembly
Path is : /usr/local/bin/bin:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
-= Rebuilding contig.fa indices =-
2031 entries from file contig.fa were indexed in file contig.fa.cidx
>>> --- clustering [contig.fa] started at Nov 4 18:53:09 2010
Launching distributed clustering:
psx -p 1 -n 1000 -i contig.fa -d cluster -C '/home/lino/Workingfolder/TGICL/contig.fa:94:30:40:' -c '/usr/local/bin/tgicl_cluster.psx'
WAITING for all children to finish before starting last child!
WAITING for all children to finish!
<<< --- clustering [contig.fa] finished at Nov 4 18:53:14 2010
Running transitive closure command: gzip -cd contig.fa_cl_tabhits_*.Z | tclust PID=94 OVL=40 OVHANG=30 -o contig.fa_cl_clusters

PID=94
OVHANG=30
OVL=40
Total t-clusters: 72
Largest cluster has 119 nodes
*** all done ***
The clusters are stored in file 'contig.fa_cl_clusters'.

>>> --- ASSEMBLE [contig.fa] started at Nov 4 18:53:14 2010
WAITING for all children to finish before starting last child!
WAITING for all children to finish!
Can't locate TGI/DBDrv/Driver/.pm in @INC (@INC contains: /usr/local/bin /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at (eval 13) line 2.
BEGIN failed--compilation aborted at (eval 13) line 2.

Package TGI:BDrv, File /usr/local/share/perl/5.10.1/TGI/DBDrv.pm, Line 42 == Can not load driver TGI:BDrv:river::!
[ TGI::Exception has been thrown ]

Can't locate TGI/DBDrv/Driver/.pm in @INC (@INC contains: /usr/local/bin /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at (eval 13) line 2.
BEGIN failed--compilation aborted at (eval 13) line 2.

Package TGI:BDrv, File /usr/local/share/perl/5.10.1/TGI/DBDrv.pm, Line 42 == Can not load driver TGI:BDrv:river::!
[ TGI::Exception has been thrown ]

Rethrow (TGI::Exception) : Package main, File /usr/local/bin/tgicl, Line 537 ==
cat: err_tgicl_contig.fa.log: No such file or directory

Process terminated with an error, at step 'ASSEMBLE'!
tgicl (contig.fa) encountered an error at step ASSEMBLE
Working directory was /home/lino/Workingfolder/TGICL.
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