DeCypher® 8.0.1 delivers wide-ranging improvements
for DeCypher and CodeQuest™ Systems

SeqCruncher™ FPGA Card Support

• Added support for SeqCruncher PCIe cards.
  
• Implemented architectural change to support SeqCruncher card features that improved performance for Tera-BLAST.
  
• Fixed a bug where padding in HMM data could get scored during HMM and HMM FrameSearch (HFST) searches on SeqCruncher cards.

Performance Improvements

• Improved performance for Tera-BLAST using translated queries or translated targets (nt to aa in 6 frames), or when using a compliment strand.
  
• Optimized Tera-BLAST to deliver additional performance increase across multiple accelerator cards.
• Further improved Tera-BLAST performance with additional code optimizations.
• Fixed bug in the score handling that could bypass Tera-BLAST performance optimizations under certain conditions.
• Improved performance of HMM searches by changing HMM raw hardware data processing to limit excessive accesses of the target database index.
• Increased query count limits for HMM searches for both G4-series and SeqCruncher cards to reflect larger hardware capacity, allowing larger models to be used.
• Improved memory usage to reduce fragmentation and allow for larger searches.
• Made additional small performance enhancements to low level code.
  

Stability Improvements

• Fixed bug that caused crashes or corrupt results when running FST searches against target loci longer than 102400 symbols.
• Improved thread pacing reporting and hardware error handling to prevent hangs due to insufficient memory.
• Improved code to prevent incorrect buffer sizing when processing hardware data.
• Fixed bug where a corrupt target database could cause a crash.
• Fixed bug that caused hang during HMM FrameSearch hardware processing.
• Fixed bug where hardware hang was not detected.
• Added additional query size checking in the Daemon to prevent a crash caused by incorrect use of the query split settings.
• Fixed job cancellation to improve response times and avoid possible crashes.
  

Accuracy Improvements

• Changed HMM scoring and statistics to be consistent with the HMMER package.
• Fixed intermittent bug that caused inconsistent results in Tera-Probe™.
• Fixed HFST to prevent inaccurate scoring.
• Fixed bug where Profile Search could get incorrect scores in hardware in rare cases.
• Improved HMM alignment accuracy in rare instances of hardware underflow.
• Fixed bug to correctly calculate statistics when submitting a matrix with a standard matrix name from a remote client with the CLI.

Functionality Improvements

• Fixed bug where using FULL as an alignment option without specifying SW was not forcing SW as it should have.
• Fixed parsing of [USERID] keyword to prevent crash.
• Removed NCBI BLAST software support from the DeCypher daemon and Web Interface.
• Added [CREATION TIME] keyword to support user-specified creation time for target databases.
• Changed html output so that links to outside pages always open in their own window or tab.
• Fixed bug with processing request files to properly rename .req file to .ack.
• Fixed bug to add necessary padding to the end of target buffers for SFI for G cards.
• Fixed bug to add frameshift penalty to the hardware code for HFST.
• Automatically detect license file changes without requiring daemon restart.
• Changed support@timelogic.com to tlsupport@activemotif.com.
• Fixed a bug that caused a numbering error in output files when countdowncomplement (on by default with Tera-BLAST) is used for large split loci.
• Fixed errors in GeneDetective templates.
• Modified dc_get_allout to give an error message if the given job is running or still queued.
• Fixed text for dc_help.
  
  

Target Building Improvements

• Fixed bug where cancelling target builds cause the wrong error to be reported.
• Fixed bug where target building could conflict with jobs running on slave systems, causing errors during the target build.
• Fixed bug where a search job could attempt to use a target that was still being built due to a synchronization error when multiple target build jobs were running at the same time.
• Fixed bug where HMM target was built incorrectly if the EVD value was missing for the model.
• Fixed a bug where a failed target build could potentially result in corrupt data used for searches
• Removed default [TARGET SET] and -targ options from format_ templates.
• Modified dc_new_target, dc_new_target_rt, and dc_make_target to require the -targ option.
• Fixed bug that delayed target builds while unrelated search jobs were running.

Error Reporting and Logging Improvements

• Added details to system.log for hardware error data.
• Improved error messages for missing or inaccessible target files.
• Improved statistics reported in benchmark file related to hardware processing.
• Fixed bug where extra error details were not reported in rare cases.
• Added logging and minimal error checking for hardware firmware versions.
• Removed redundant generation of log entries for target databases when they are copied to slave computers.
• Minor improvements to query and target write error reporting.
• Improved hardware related error reporting.
• Improved error reporting for incorrectly formatted license files
• Improved version tracking of hardware definition files.
• Added additional checking to ensure accelerator firmware is up to date.
• Added functionality to update SeqCruncher card firmware.
  
  

Important Notes:

1. It is possible that HMM target databases built before this release of DeCypher 8.0.1 may have incorrect EVD information which can effect statistics calculations. This only occurred when the original HMM data used to build the target database had EVD values for some models but not for others.

We recommend that all HMM target databases be rebuilt if there is a chance that your data inconsistently included EVD values for some models but not others. Additionally, if you have HMM target databases that were built with a version of DeCypher older than 7.6.2, you should rebuild all of those databases due to other fixes that were reported in release 7.6.2.

2. The Semi-Global Smith-Waterman (SGSW) algorithm is no longer supported and has been removed from the product.

3. [SCALE FACTOR] is no longer supported. Applying [SCALE FACTOR] values other than “1” which allowed more accurate scoring with matrices containing non-integer values is no longer supported.

Important note for SeqCruncher card systems:

1. There has been a format change to HMM and Profile databases in DeCypher 8.0.1 running on SeqCruncher accelerator cards.

HMM and Profile target databases built with earlier releases of DeCypher may need to be rebuilt for systems with SeqCruncher cards if the HMM or profile database contains at least one profile or model with less than 16 symbols.

The following error will be reported in this situation to alert you that rebuilding the database is required:

Error=3572-00-00 The database is an older format and contains one or more loci that have an incorrect size format.

Please contact TimeLogic support if you have any questions on the installation or features in this release.