Celera Assembler runCA failed

[DNAjunk]

Hello

I would like to use the Celera assembler on a small data set for testing the installation.

First, I made the frg file based on the sff file
~/apps/Celera/c/sffToCA -libraryname 0 -output my001.1.frg F032I7H01.sff

Then, runCA
~/apps/Celera/c/runCA -p t -d . my001.1.frg

The end of output, shortly before the error happens is:

----------------------------------------START CONCURRENT Tue Sep 8 09:27:41 2009
/data/Celera/my001.1-test/./5-consensus/consensus.sh 1 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 2 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 3 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 4 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 5 > /dev/null 2>&1
----------------------------------------END CONCURRENT Tue Sep 8 09:31:57 2009 (256 seconds)
/data/Celera/my001.1-test/./5-consensus/t_002 failed -- no .success or no .cgi!
================================================================================

runCA failed.

----------------------------------------
Stack trace:

at /home/apps/Celera/c/runCA line 1005
main::caFailure('1 consensusAfterUnitigger jobs failed', 'undef') called at /home/apps/Celera/c/runCA line 2252
main:ostUnitiggerConsensus('/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...') called at /home/apps/Celera/c/runCA line 4988

----------------------------------------
Failure message:

1 consensusAfterUnitigger jobs failed


Does anybody have a solution?

Thank you for your suggestions!

[sklages]

Hello

I would like to use the Celera assembler on a small data set for testing the installation.

First, I made the frg file based on the sff file
~/apps/Celera/c/sffToCA -libraryname 0 -output my001.1.frg F032I7H01.sff

Then, runCA
~/apps/Celera/c/runCA -p t -d . my001.1.frg

What version of CA you are using?

The end of output, shortly before the error happens is:

----------------------------------------START CONCURRENT Tue Sep 8 09:27:41 2009
/data/Celera/my001.1-test/./5-consensus/consensus.sh 1 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 2 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 3 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 4 > /dev/null 2>&1
/data/Celera/my001.1-test/./5-consensus/consensus.sh 5 > /dev/null 2>&1
----------------------------------------END CONCURRENT Tue Sep 8 09:31:57 2009 (256 seconds)
/data/Celera/my001.1-test/./5-consensus/t_002 failed -- no .success or no .cgi!
================================================================================

runCA failed.

----------------------------------------
Stack trace:

at /home/apps/Celera/c/runCA line 1005
main::caFailure('1 consensusAfterUnitigger jobs failed', 'undef') called at /home/apps/Celera/c/runCA line 2252
main:ostUnitiggerConsensus('/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...', '/data/Celera/my001.1-test/./4-unitigge...') called at /home/apps/Celera/c/runCA line 4988

----------------------------------------
Failure message:

1 consensusAfterUnitigger jobs failed


Does anybody have a solution?

Thank you for your suggestions!

You should have a look at http://sourceforge.net/apps/mediawik...sensus_failure

Let us know, if this has worked for you.

cheers,
Sven

[DNAjunk]

Thanks for your response.
1)
The version is

[my001.1-test] ~/apps/Celera/c/runCA -version
CA version 5.4 ($Id: AS_GKP_main.c,v 1.79 2009/03/05 18:36:04 skoren Exp $).
CA version 5.4 ($Id: AS_OVL_overlap_common.h,v 1.54 2009/05/21 02:24:37 brianwalenz Exp $).
CA version 5.4 ($Id: AS_CGB_unitigger.c,v 1.38 2009/05/21 02:24:37 brianwalenz Exp $).
CA version 5.4 ($Id: BuildUnitigs.cc,v 1.57 2009/02/02 13:51:13 brianwalenz Exp $).
CA version 5.4 ($Id: AS_CGW_main.c,v 1.70 2009/05/11 05:36:03 brianwalenz Exp $).
CA version 5.4 ($Id: Consensus_CNS.c,v 1.77 2009/05/21 03:50:03 brianwalenz Exp $).
CA version 5.4 ($Id: AS_TER_terminator.c,v 1.30 2008/10/29 06:34:30 brianwalenz Exp $).

2)
There is no 'Project'_xxx.failed but another "failed"-file called t_002.autofix.cgi.failed

This is the content of the 5-consensus directory:
t.partFile
t.partitioned.err
t.partitioned
consensus.sh*
consensus.cgi.input
t_002.autofix.orig
t_001.success
t_001.err
t_001.cgi
t_002.err
t_002.cgi
t_002.autofix.log
t_002.autofix.err
t_002.autofix.cgi.failed
t_002.autofix.cgi
t_002.autofix
t_003.success
t_003.err
t_003.cgi
t_004.success
t_004.err
t_004.cgi
t_005.success
t_005.err
t_005.cgi

And the 4-unitigger directory:
best.edges
best.contains
t.breaks.ovl
unitigger.success
unitigger.err
t.unused.ovl
t.iidmap
t.cga.0
t_005.cgb
t_004.cgb
t_003.cgb
t_002.cgb
t_001.cgb


I couldn't find anything related to "autofix.cgi.failed".

By the way, I didn't install the perl statistics module yet. But I guess the current error is due to something else.