v1.6.5post1

• Changed conda package recipe to depend only on the conda-forge and bioconda channels.

v1.6.5

• Fix a bug in which --cleaning would only use one pair of files per sample, even if more were specified in the samples file.
• Fixed a bug in which the pipeline would stop with an error at step 10 if the number of mapped reads was too low.
• This is a fast release aimed to fix a couple of bugs. We have not updated SQMtools or the PDF manual so they both reflect version 1.6.3.

v1.6.4

• This changes the way that bin disparity is calculated. Now it will be simply the ratio of contigs disagreeing with the consensus taxonomy. This is faster and leads to comparable results overall. This also fix an issue in which very large bins (such as eukaryotic bins) may consume a lot of memory during step 16.
• This is a fast release aimed to fix a single bug. We have not updated SQMtools or the PDF manual so they both reflect version 1.6.3.

v1.6.3

• Conda installations will now prioritize conda binaries instead of the vendored ones in some cases. This will hopefully fix certain issues in which SqueezeMeta was failing on certain distributions/versions.
• test_install.pl now performs additional tests to check that binaries can be executed in the current environment.
• Increased speed and reduced memory usage in step 10 (read counting).
• Fixed an error in which projects created with the sequential mode would fail to restart. Note that each sample still has to be restarted individually.
• Fixed an error in which step 16 (DAStool bin merging) would be attempted even if the --nobins flag was provided.
• SQMtools: fixed an error in exportPathways when the requested KEGG map had only arrows.
• SQMtools: fixed an error in which figures would not generated properly when `count='percent' was selected if any sample had 0 reads (as could happen when analyzing subsets).

v1.6.2post3

• Update SPAdes to 3.15.5 so it works with python 3.10

v1.6.2post2

• Upgrade to python 3.10 and improve conda packaging, hopefully fix #705 and be more future-proof

v1.6.2post1

• Fix an issue in which pysam was not properly installed when installing SqueezeMeta through conda

v1.6.2

New features

• Added spades-base as a possible assembler for SqueezeMeta. This will make SqueezeMeta call SPAdes with no additional flags. Flags for SPAdes can then customized by the user by passing --assembly_options "EXTRA OPTIONS" when calling SqueezeMeta. More information can be found in the ReadMe and the PDF manual.
• Added the utility script sqm2zip.py, which allows to pack the essential files from a SqueezeMeta project into a single zip file.
• SQMtools: loadSQM can now load a project directly from a zip file created by sqm2zip.py (syntax would be `loadSQM("/path/to/my_project.zip").
• SQMtools: SQMtools is now available in CRAN and can be installed with install.packages("SQMtools") in Windows, Mac and Linux computers.
• These changes are meant to allow users to easily transfer their data from their clusters/workstations to their personal computers and explore their results there.
• SQMtools: mostAbundant and mostVariable now accept the argument bycol = TRUE, which will make these functions operate on columns rather than rows.

Minor changes / bugfixes

• We now use coverage variances in addition to average contig coverages when calling metabat2, which should improve the quality of the resulting bins.
• Mapping results are now stored as BAM files instead of SAM files, which should reduce disk usage.

Known issues / Other announcements

• The make_databases.pl script may spend a lot of time in the "Creating SQLite databases" step. We have included a patch to improve this, but still it happens inconsistently (taking a few hours in some systems, and several days in others). Having a lot (1-2 Tb) of free disk space may help. download_databases.pl should be considered as the preferred way of quickly getting reasonably-up-to-date databases.
• We are discontinuing official support for CentOS7, as its default libraries are too outdated now. We plan on supporting SqueezeMeta in Debian, WSL2-Ubuntu and (hopefully) CentOS Upstream in the not so distant future.

v1.6.1post1

• Fix for yesterday's release, which did not include all the intended features.

v1.6.1

New features

• Added the seqvec2fasta function to SQMtools. It will print a named vector containing sequences (as the ones used to store contig and ORF sequences in SQM$contigs$seqs and SQM$orfs$seqs as a single fasta-formatted string.
• The make_databases.pl, download_databases.pl and configure_nodb.pl scripts now perform more error checking after each database creation step, and will call test_install.pl before finishing. This should help detect the instances in which database creation was unsuccessful e.g. due to a failed download.

Minor changes / bugfixes

• Fixed a bug in remap.pl.
• Fixed a bug introduced in v1.6.0 in which trimmomatic was not being called even when the --cleaning flag was provided.
• Fixed a bug in which single reads were causing problems during assembly.
• Fixed a bug in which cover.pl was using the system's perl interpreter instead the one in the user environment.
• Improved SQL queries in make_databases.pl to hopefully speed up database creation.
• Fixed an issue in which mothur dependencies were not correctly fulfilled by conda.
• Fixed an issue in which restarting a sequential project failed at step 4.
• Fixed several minor issues with the restart mode.
• Fixed remove_duplicate_markers.pl so it works in the new binning structure.
• Fixed an issue in which SPAdes was using only 400G of memory even if more was available in the system.
• engine="data.table and tax_mode="prokfilter" are now the default options in loadSQM.
• Fixed an issue in which subsetSamples corrupted the binning information, making it impossible to further subset the resulting object.
• The PDF SQMtools manual is back. Future availability will depend on whether I can keep getting R's clunky latex interface to produce PDF's in which the tables are rendered correctly.

Known issues

• The make_databases.pl may spend a lot of time in the "Creating SQLite databases" step. We have included a patch to improve this, but still it happens inconsistently (taking a few hours in some systems, and several days in others). Having a lot (1-2 Tb) of free disk space may help. download_databases.pl should be considered as the preferred way of quickly getting reasonably-up-to-date databases.