update archaeal market set

README.md

@@ -19,7 +19,7 @@ Please post questions and issues related to GTDB-Tk on the Issues section of the
 ## New Features
 
 GTDB-Tk v2.1.0 includes the following new features:
-- GTDB-TK now uses a **divide-and-conquer** approach where the bacterial reference tree is split into multiple **class**-level subtrees. This reduces the memory requirements of GTDB-Tk from **320 GB** of RAM when using the full GTDB R07-RS207 reference tree to approximately **50 GB**. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the `--full-tree` flag.  
+- GTDB-TK now uses a **divide-and-conquer** approach where the bacterial reference tree is split into multiple **class**-level subtrees. This reduces the memory requirements of GTDB-Tk from **320 GB** of RAM when using the full GTDB R07-RS207 reference tree to approximately **55 GB**. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the `--full-tree` flag.  
 This is the main change from v2.0.0. The split tree approach has been modified from order-level trees to class-level trees to resolve specific classification issues (See [#383](https://github.com/Ecogenomics/GTDBTk/issues/383)). 
 - Genomes that cannot be assigned to a domain (e.g. genomes with no bacterial or archaeal markers or genomes with no genes called by Prodigal) are now reported in the `gtdbtk.bac120.summary.tsv` as 'Unclassified'
 - Genomes filtered out during the alignment step are now reported in the `gtdbtk.bac120.summary.tsv` or `gtdbtk.ar53.summary.tsv` as 'Unclassified Bacteria/Archaea'

docs/src/changelog.rst

@@ -8,7 +8,7 @@ Change log
 
 Major changes:
 
-* GTDB-TK now uses a **divide-and-conquer** approach where the bacterial reference tree is split into multiple **class**-level subtrees. This reduces the memory requirements of GTDB-Tk from **320 GB** of RAM when using the full GTDB R07-RS207 reference tree to approximately **50 GB**. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the `--full-tree` flag. This is the main change from v2.0.0. The split tree approach has been modified from order-level trees to class-level trees to resolve specific classification issues (see `#383 <https://github.com/Ecogenomics/GTDBTk/issues/383>`_).
+* GTDB-TK now uses a **divide-and-conquer** approach where the bacterial reference tree is split into multiple **class**-level subtrees. This reduces the memory requirements of GTDB-Tk from **320 GB** of RAM when using the full GTDB R07-RS207 reference tree to approximately **55 GB**. A manuscript describing this approach is in preparation. If you wish to continue using the full GTDB reference tree use the `--full-tree` flag. This is the main change from v2.0.0. The split tree approach has been modified from order-level trees to class-level trees to resolve specific classification issues (see `#383 <https://github.com/Ecogenomics/GTDBTk/issues/383>`_).
 * Genomes that cannot be assigned to a domain (e.g. genomes with no bacterial or archaeal markers or genomes with no genes called by Prodigal) are now reported in the `gtdbtk.bac120.summary.tsv` as 'Unclassified'
 * Genomes filtered out during the alignment step are now reported in the `gtdbtk.bac120.summary.tsv` or `gtdbtk.ar53.summary.tsv` as 'Unclassified Bacteria/Archaea'
 * `--write_single_copy_genes` flag in now available in the `classify_wf` and `de_novo_wf` workflows.

docs/src/installing/index.rst

@@ -38,7 +38,7 @@ Hardware requirements
      - ~65 GB
      - ~1 hour / 1,000 genomes @ 64 CPUs
    * - Bacteria
-     - ~320 GB ( 20GB for divide-and-conquer)
+     - ~320 GB ( 55GB for divide-and-conquer)
      - ~65 GB
      - ~1 hour / 1,000 genomes @ 64 CPUs
 
@@ -137,9 +137,12 @@ Note that different versions of the GTDB release data may not run on all version
    * - GTDB Release
      - Minimum version
      - Maximum version
+   * - R207_v2
+     - 2.1.0
+     - Current
    * - R207
      - 2.0.0
-     - Current
+     - 2.0.0
    * - R202
      - 1.5.0
      - 1.7.0

gtdbtk/classify.py

@@ -256,7 +256,7 @@ def place_genomes(self,
         if levelopt is None or levelopt == 'high':
             self.logger.info(f'pplacer version: {pplacer.version}')
         # #DEBUG line
-        run_pplacer = False
+        run_pplacer = True
         if run_pplacer:
             pplacer.run(self.pplacer_cpus, 'wag', pplacer_ref_pkg, pplacer_json_out,
                         user_msa_file, pplacer_out, pplacer_mmap_file)