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.