This page contains (mostly) all of the changes that were made between each version of EnTAP. The current latest version is EnTAP Beta v0.10.8-beta
- Optimizations made to similarity searching using the EnTAP SQL database. Should improve speed
- Added 'api-taxon' command that will verify whether an input taxon can be found in the taxonomy database. It will return json formatted text
- Added additional messaging throughout EnTAP execution to stdout
- Removed Test Data from repository, it is no longer compatible with latest version of software within EnTAP. Will add back an updated dataset next version
- Changed DIAMOND command to use '--max-target-seqs' instead of '--top' command
- Fixed an issue where duplicate sequences were printed to the final_annotations files
- Fixed an issue where the taxanomic species may not have been found when searching against the SQL EnTAP database
- This version requires a new version of the EnTAP database to be downloaded
- Added Gene Enrichment files as an output option(gene ID + effective length and geneID + GO term). These can be seen with the output-type flag in the ini file
- Changed Gene Ontology level printing. 0 will continue to print every term. Other levels will now print that level AND higher. So a level of 1 will print 1, 2, 3, etc. Previous a level of 1 would only print GO Terms with a level of 1
- Changed 'uninformative' input from a file to a list of terms in the ini file. Much more straightforward this way
- If no alignments are found against a database during DIAMOND, the pipeline will no longer exit, it will continue to the next database. If no alignments are found against any databases, it will stop at that point
- Fixed a bug where TransDecoder output may not have been parsed correctly for some users. This presented itself as a parsing error and halted EnTAP at that stage of the pipeline
- Fixed bug where InterProScan Mobidlite database was giving an error for some users (and halting execution)
- Fixed an issue where certain sequence headers may not have been parsed properly resulting in unrecognized sequence errors during Similarity Searching
- Added support to pipe the TransDecoder flag '--no_refine_starts' during Execution
- Fixed an issue where error messages during EggNOG searching would not get printed (seg fault)
- Contaminant information will not be printed to the log if there are none
- Added a step to remove the stop codon ('*') sometimes printed at the end of the TransDecoder FASTA output. This may have caused an issue when running TransDecoder and InterProScan together
- Fixed an issue where expression analysis transcriptome generation would fail (error message presented to user as 'frame selection')
- Fixed a parsing issue of user inputs for contanminants and taxon
- Fixed a pathing issue when EnTAP generated frame selected transcriptomes
Note: Please use v0.10.2-beta or later instead of this version
- Added support for TransDecoder for Frame Selection
- Added TPM as an additional output from Expression Filtering
- Added an .ini file and moved many commands/paths from the command line to this
- Standardized/finalized output header namings for gFACs support
- Changed the default Frame Selection software to TransDecoder. GeneMarkS-T can still be selected through the .ini file
- Changed the default Gene Ontology level to 1. This can be easily changed through the ini file
- Fixed issue where some EggNOG descriptions were not printed to the final output
- Fixed a few issues with older GCC versions
- Fixed an issue where GeneMarkS-T would write to the working directory
- Updated EggNOG Database links
- 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
- 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 (August 2, 2018) -------------------------------------
- Fixed an issue when inputting already translated sequences
- Minor bug fixes
- Changes to CMake to hopefully resolve issues a couple users had with linking to Boost Libraries
- 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 (April 14, 2018) --------------------------------------
- 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 (December 16, 2017) -----------------------------
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 (September 5, 2017) -------------------------------
- Minor changes to taxonomic database download and indexing
EnTAP Beta v0.7.4-beta (August 26, 2017) ----------------------------------
- Initial beta release!