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.
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:
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
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.
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.
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:
Code:
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.
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
Code:
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
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.
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