Changelog¶
This page contains (mostly) all of the changes that were made between each version of EnTAP. The current latest version is EnTAP Beta v0.9.1-beta
EnTAP Beta v0.9.1-beta¶
- Changed –trim flag to –no-trim. Trimming sequence headers to the first space is the default now. If you have executions from previous versions, you may need to use the –no-trim flag as needed for backwards compatibility (picking up where you left off).
- Fixed a bug where the –single-end command was not properly recognized.
EnTAP Beta v0.9.0-beta¶
- This release focused on reducing installation complexity and removing dependencies
- Overhauled the configuration/execution process by removing EggNOG-mapper and replacing it with an internal EnTAP method. This will make installation and both stages much clearer for the user
- Removed Boost Libraries from dependencies further reducing installation complexity
- Added printing of error messages to the standard log from any software being used by EnTAP. This will make debugging much easier
- Added UniProt mapping to the EnTAP database. This will pull any additional mapping information from UniProt Swiss-Prot alignments
- Updated supported DIAMOND version to 0.9.9
- The EnTAP database MUST be re-configured for this release
- Resolved any incompatibility with DIAMOND and EggNOG databases as well as versioning problems
- Standardized EnTAP log entries and added additional statistics
- -ontology flag will now use EnTAP’s method of EggNOG accession (0) or InterProScan (1)
- Bug fixes
EnTAP Beta v0.8.4-beta¶
- Fixed an issue when inputting already translated sequences
EnTAP Beta v0.8.3-beta¶
- Minor bug fixes
- Changes to CMake to hopefully resolve issues a couple users had with linking to Boost Libraries
EnTAP Beta v0.8.2-beta¶
- Revamped configuration stage of EnTAP (reduced time and hopefully made things clear/more compatible across systems)
- Removed - -database-out flag (seemed a bit redundant to me). - -outfiles flag will be the default when indexing databases
- Added - -data-generate flag. This can be specified in EnTAP config stage (no effect during execution) for whether you’d like to generate the EnTAP databases rather than downloading from FTP address
- Added - -data-type flag. This can be used in either configuration or execution. Specifies which database you’d like to download/generate or use during execution. Binary (0, default) or SQL (1). Binary is faster with more memory usage, SQL will be slower but easier compatibility.
- Combined EnTAP databases into one (entap_database.sql/entap_database.bin). WARNING: Re-download or configuration of databases is REQUIRED with this newer version.
- Removed download_tax.py script (no longer necessary)
EnTAP Beta v0.8.1-beta¶
- Added additional error logging to provide more information when something goes wrong
- Configuration file mandatory (default place to look is current working directory)
- Changed tax database paths in config file to avoid confusion (separate text and bin). Config file must be re-downloaded/generated!
- Defaults/output during configuration changed to config file then if not found, database-out flag
- Added deletion of empty files if a certain stage failed (preventing re-reading an empty file)
- Added errors/warnings for no alignments/hits in each stage
- entap_out directory changed to transcriptomes to be more clear (holds only transcriptomic data)
- Final EnTAP output files moved from the root outfiles directory to final_results directory
- Several filename changes to add consistency in new transcriptomes directory (final transcriptome is now _final.fasta.
- Several title changes to the log file to mitigate confusion
- EggNOG no longer broken down into separate files - those that hit and those that did not hit a database. Now entire transcriptome is pushed with one output file
- 10 species/contaminants/other in similarity searching statistics has been changed to 20 to provide more information to the user
- Best hit selection state combined with similarity search
- Added ‘N’ as an accepted nucleotide
- Several behind the scenes changes
- Fixed Cmake global installation issue
- Fixed incorrect error codes
- Fixed InterPro printing bug to no hits/hits files
- Fixed Frame Selection not printing new lines for certain files
EnTAP Beta v0.8.0-beta¶
Overhaul of the taxonomic/gene ontology databases
- Faster accession/indexing
- MUST be re-downloaded and re-indexed (or use the updated versions that come with the EnTAP distribution)
- Taxonomic database includes thousands more entries with synonyms of many species
- Perl is no longer a dependency, with Python being used to download the database
Added blastx support
- Blastx now allowed for ALL stages of annotation (similarity search + ontology)
- –runN flag now specifies blastx (frame selection will not be ran)
- –runP flag now specifies blastp (frame selection will be performed if nucleotide sequences are input)
Added InterProScan support
- Now possible to run EggNOG and/or InterProScan (with both blastx or blastp)
- EggNOG and/or InterProScan specified with –ontology flag (0 and/or 1)
- Full output of both will be provided in the final annotations file
Added additional statistics to the log file for EggNOG and Expression Analysis
Added numerous file/path/software checks to the start of an EnTAP run
- Test runs/path checks are performed on all software that will be ran
- Additional checks to specific flags
- These checks can be turned off for an EnTAP run with –no-check flag (not advised!)
–tag flag changed to –out-dir to specify output directory (not just what you’d like it named as)
- Defaults to current directory with /outfiles folder
–paired-end flag for Expression Filtering changed to –single-end (with paired-end being the default)
Added contaminant and informative yes/no columns in final annotations file (among other headers)
Added ability to input your own list of informative/uninformative terms for EnTAP to flag
Added contaminant and none contaminant final annotation files
Fixed a sequence id issue in Expression Filtering not mapping to BAM/SAM file
Fixed a bug in –trim flag for sequence headers
Fixed a bug where some systems had issues with graphing
Debug and log files are now time stamped and not overwritten
Fixed pathing for EnTAP configuration and made more streamlined
Fixed several instances of older compilers complaining
Added a lot of error messaging to help diagnose any issues easily
Changed similarity search to have full database name, not path
Fixed a bug in parsing input fasta file (added corrupt file checks)
EnTAP Beta v0.7.4.1-beta¶
- Minor changes to taxonomic database download and indexing
EnTAP Beta v0.7.4-beta¶
- Initial beta release!