WGS 7.0 (CABOG) fails on consensus step

[Jens Hooge]

Hello,

I'm relatively new to NGS and its tools, but at the moment I'm trying to run an assembly of a mix of single ended and paired ended 454 reads using the
wgs-7.0-assembler.

http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page

I have converted a number of FASTQ files to FRG files using CABOGs fastqToCA routine.
Because I got single and paired end reads I converted in case of paired end reads with
different mean insert sizes and standard deviations. For each of my FASTQ files I called
fastqToCA with the same library name ("LIB" in that case).

The last lines of melonAssembly.gkpStore.err are as follows:

Starting file '/home1/jens/workspace/Computomics/src/bcs03/melonAssembly/FRG/corrected/GN7J8A002-corrected.frg'.

Processing INNIE SANGER QV encoding reads from:
      '/tmp2/bcs03/melonFastqCorrected/paired/GN7J8A002-corrected.fastq' (INTERLACED)
GKP finished with 11339518 alerts or errors:
11338139        # ILL Error: not a sequence start line.
1292    # ILL Error: not a quality start line.
19      # LIB Alert: suspicious mean and standard deviation; reset stddev to 0.10 * mean.
68      # LIB Alert: already exists; can't add it again.

Besides the LIB alerts the ILL errors seem suspicious but a validation of my FASTQ files
for format consistency resulted in no errors so I just gave it a go and went on.
Edit: The ILL errors are thrown because of read lengths above 2047 bps. A bug that's supposed to be fixed since wgs-7.0.
(see: http://sourceforge.net/apps/mediawik..._Release_Notes)

"Gatekeeper: Numerous problems with reads longer than the maximum allowed (2047bp) and reads of very specific lengths were discovered and fixed. All of these resulted in gatekeeper crashing."

However after I called runCA with my FRG files it aborted at step 5-consensus-insert-sizes with
an error message saying

ERROR: Failed with signal ABRT (6)
================================================================================

runCA failed.

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

 at /ctx/galaxy/galaxyTools/tools/wgs-7.0/Linux-amd64/bin/runCA line 1237
	main::caFailure('Insert size estimation failed', '/tmp2/bcs03/melonAssembly/DATA/melonAssembly/5-consensus-inse...') called at /ctx/galaxy/galaxyTools/tools/wgs-7.0/Linux-amd64/bin/runCA line 4550
	main::postUnitiggerConsensus() called at /ctx/galaxy/galaxyTools/tools/wgs-7.0/Linux-amd64/bin/runCA line 5883

----------------------------------------
Last few lines of the relevant log file (/tmp2/bcs03/melonAssembly/DATA/melonAssembly/5-consensus-insert-sizes/estimates.out):

Loading fragment information  10000000 out of  14499910
tigStore: MultiAlignMatePairAnalysis.C:173: void matePairAnalysis::evaluateTig(MultiAlignT*): Assertion `0' failed.
Aborted (core dumped)

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

Insert size estimation failed

After reading some bug reports I deleted the folders 5-consensus, 5-consensus-insert-sizes
and melonAssembly.tigStore and ran runCA again with the same parameters as in my first run.
I would very much appreciate for some help on how to resolve these errors.

[sklages]

In this case I'd contact the developers directly. They are usually very helpful. We had quite a few issues in the past with CA but everything could be solved with their help.
Most of the "problems" were very specifc, not very generic :-)

But you should post the solution here back to the forum ...

my 2p,
Sven