PICRUSt2 v2.3.0-b

Major changes

• Now screen out study sequences that align poorly to reference sequences (taken to be 80% of original length by default). These sequences aren't placed at all and are listed in standard error.

• Fixed bug where a mix of integers and floats were all converted to floats when used as sequence ids.

Minor changes

• Improved how stderr and stdout of subprocess commands is captured when running picrust2_pipeline.py.

• Will output range of study sequence lengths when --verbose option set.

• Bumped r-castor version from 1.4.1 to 1.5.0

• Bumped epa-ng version from 0.3.5 to 0.3.6

• Bumped gappa version from 0.4.0 to 0.5.1

• Set required hmmer version range to be >=3.1.b2,<=3.2.1 rather than just 3.2.1 (Confirmed that study sequence alignments are identical with these three hmmalign versions: 3.1b2, 3.2, 3.2.1)

• Will now check for a column called "taxonomy" and throw a warning if it exists.

• Added more verbose options and changed option to be --verbose rather than --print_cmds for clarity in individual scripts.

• Throw error if space found in input FASTA filepath (causes problems for downstream placement tools)

• Create pipeline output directory after running basic sanity checks (like checking that all files exist)

• Set upperbound of 0.25.0 for pandas version for now to avoid massive spike in system time usage with newest versions