Merge pull request #105 from Ecogenomics/master

mmap-file fixed
Ecogenomics · Mar 18, 2019 · edca6e2 · edca6e2
2 parents 2bd8a00 + 0c8fb02
commit edca6e2
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diff --git a/gtdbtk/VERSION b/gtdbtk/VERSION
@@ -1,3 +1,5 @@
+0.2.2
+- Fix support for writing to a scratch file using pplacer (--mmap-file options).
 0.2.1
 - remove Perl dependencies
 - remove Biolib,mpdl3,jinja dependencies

diff --git a/gtdbtk/classify.py b/gtdbtk/classify.py
@@ -123,11 +123,12 @@ def place_genomes(self,
         pplacer_json_out = os.path.join(
             pplacer_out_dir, 'pplacer.{}.json'.format(marker_set_id))
 
-        cmd = 'pplacer -j {} -c {} -o {} {} > {} 2>&1'.format(self.cpus,
-                                                              pplacer_ref_pkg,
-                                                              pplacer_json_out,
-                                                              user_msa_file,
-                                                              pplacer_out)
+        cmd = 'pplacer -j {} -c {}{} -o {} {} > {}'.format(self.cpus,
+                                                           pplacer_ref_pkg,
+                                                           pplacer_mmap_file,
+                                                           pplacer_json_out,
+                                                           user_msa_file,
+                                                           pplacer_out)
 
         os.system(cmd)