Changelog

This page contains (mostly) all of the changes that were made between each version of EnTAP. The current latest version is EnTAP Beta v0.9.0-beta

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!