Merge pull request #572 from nextstrain/keep-logs

Keep log files produced by augur tree

augur/tree.py

@@ -70,7 +70,6 @@ def build_raxml(aln_file, out_file, clean_up=True, nthreads=1, tree_builder_args
         if clean_up:
             os.remove("RAxML_bestTree.%s"%(random_string))
             os.remove("RAxML_info.%s"%(random_string))
-            os.remove("RAxML_log.%s"%(random_string))
             os.remove("RAxML_parsimonyTree.%s"%(random_string))
             os.remove("RAxML_result.%s"%(random_string))
 
@@ -118,8 +117,6 @@ def build_fasttree(aln_file, out_file, clean_up=True, nthreads=1, tree_builder_a
     try:
         run_shell_command(cmd, raise_errors = True, extra_env = extra_env)
         T = Phylo.read(out_file, 'newick')
-        if clean_up:
-            os.remove(log_file)
     except:
         print("ERROR: TREE BUILDING FAILED")
         if os.path.isfile(log_file):
@@ -189,11 +186,10 @@ def build_iqtree(aln_file, out_file, substitution_model="GTR", clean_up=True, nt
             if substitution_model.lower() == 'none':
                 shutil.copyfile(log_file, out_file.replace(out_file.split('/')[-1],"iqtree.log"))
 
-            for f in [log_file, tmp_aln_file]:
-                if os.path.isfile(f):
-                    os.remove(f)
+            if os.path.isfile(tmp_aln_file):
+                os.remove(tmp_aln_file)
 
-            for ext in [".bionj",".ckp.gz",".iqtree",".log",".mldist",".model.gz",".treefile",".uniqueseq.phy",".model"]:
+            for ext in [".bionj",".ckp.gz",".iqtree",".mldist",".model.gz",".treefile",".uniqueseq.phy",".model"]:
                 if os.path.isfile(tmp_aln_file + ext):
                     os.remove(tmp_aln_file + ext)
     except:

tests/builds/zika.t

@@ -10,7 +10,7 @@ Running from the test data directory allows us to use relative paths that won't
 
 Parse a FASTA whose defline contains metadata into separate sequence and metadata files.
 
-  $ augur parse \
+  $ ../../../bin/augur parse \
   >   --sequences "data/zika.fasta" \
   >   --output-sequences "$TMP/out/sequences.fasta" \
   >   --output-metadata "$TMP/out/metadata.tsv" \
@@ -21,7 +21,7 @@ Parse a FASTA whose defline contains metadata into separate sequence and metadat
 
 Filter sequences by a minimum date and an exclusion list and only keep one sequence per country, year, and month.
 
-  $ augur filter \
+  $ ../../../bin/augur filter \
   >   --sequences "results/sequences.fasta" \
   >   --metadata "results/metadata.tsv" \
   >   --exclude "config/dropped_strains.txt" \
@@ -35,7 +35,7 @@ Filter sequences by a minimum date and an exclusion list and only keep one seque
 
 Align filtered sequences to a specific reference sequence and fill any gaps.
 
-  $ augur align \
+  $ ../../../bin/augur align \
   >  --sequences "results/filtered.fasta" \
   >  --reference-sequence "config/zika_outgroup.gb" \
   >  --output "$TMP/out/aligned.fasta" \
@@ -45,7 +45,7 @@ Align filtered sequences to a specific reference sequence and fill any gaps.
 
 Build a tree from the multiple sequence alignment.
 
-  $ augur tree \
+  $ ../../../bin/augur tree \
   >  --alignment "results/aligned.fasta" \
   >  --output "$TMP/out/tree_raw.nwk" \
   >  --method iqtree \
@@ -54,9 +54,15 @@ Build a tree from the multiple sequence alignment.
   $ python3 "$TESTDIR/../../scripts/diff_trees.py" "results/tree_raw.nwk" "$TMP/out/tree_raw.nwk" --significant-digits 5
   {}
 
+Confirm that tree log file exists.
+
+  $ test -e "results/aligned-delim.iqtree.log"
+  $ echo $?
+  0
+
 Build a time tree from the existing tree topology, the multiple sequence alignment, and the strain metadata.
 
-  $ augur refine \
+  $ ../../../bin/augur refine \
   >  --tree "results/tree_raw.nwk" \
   >  --alignment "results/aligned.fasta" \
   >  --metadata "results/metadata.tsv" \
@@ -81,7 +87,7 @@ Branch lengths and other annotations like dates are too stochastic across runs t
 
 Calculate tip frequencies from the tree.
 
-  $ augur frequencies \
+  $ ../../../bin/augur frequencies \
   >  --method kde \
   >  --tree "results/tree.nwk" \
   >  --metadata "results/metadata.tsv" \
@@ -92,7 +98,7 @@ Calculate tip frequencies from the tree.
 
 Infer ancestral sequences from the tree.
 
-  $ augur ancestral \
+  $ ../../../bin/augur ancestral \
   >  --tree "results/tree.nwk" \
   >  --alignment "results/aligned.fasta" \
   >  --infer-ambiguous \
@@ -103,7 +109,7 @@ Infer ancestral sequences from the tree.
 
 Infer ancestral traits from the tree.
 
-  $ augur traits \
+  $ ../../../bin/augur traits \
   >  --tree "results/tree.nwk" \
   >  --weights "config/trait_weights.csv" \
   >  --metadata "results/metadata.tsv" \
@@ -123,7 +129,7 @@ See augur issue 541 (https://github.com/nextstrain/augur/issues/541) for more de
 
 Translate inferred ancestral and observed nucleotide sequences to amino acid mutations.
 
-  $ augur translate \
+  $ ../../../bin/augur translate \
   >  --tree "results/tree.nwk" \
   >  --ancestral-sequences "$TMP/out/nt_muts.json" \
   >  --reference-sequence "config/zika_outgroup.gb" \
@@ -133,7 +139,7 @@ Translate inferred ancestral and observed nucleotide sequences to amino acid mut
 
 Export JSON files as v1 auspice outputs.
 
-  $ augur export v1 \
+  $ ../../../bin/augur export v1 \
   >  --tree "results/tree.nwk" \
   >  --metadata "results/metadata.tsv" \
   >  --node-data "$TMP/out/branch_lengths.json" \
@@ -146,15 +152,15 @@ Export JSON files as v1 auspice outputs.
   >  --output-meta "$TMP/out/v1_zika_meta.json" \
   >  --output-sequence "$TMP/out/v1_zika_seq.json" > /dev/null
 
-  $ augur validate export-v1 "$TMP/out/v1_zika_meta.json" "$TMP/out/v1_zika_tree.json" > /dev/null
+  $ ../../../bin/augur validate export-v1 "$TMP/out/v1_zika_meta.json" "$TMP/out/v1_zika_tree.json" > /dev/null
 
 Compare auspice metadata files, but ignore the "updated" field since this changes with the date the export command is run.
 
   $ diff -u --ignore-matching-lines updated "auspice/v1_zika_meta.json" "$TMP/out/v1_zika_meta.json"
 
 Export JSON files as v2 auspice outputs.
 
-  $ augur export v2 \
+  $ ../../../bin/augur export v2 \
   >  --tree "results/tree.nwk" \
   >  --metadata "results/metadata.tsv" \
   >  --node-data "$TMP/out/branch_lengths.json" \
@@ -167,7 +173,7 @@ Export JSON files as v2 auspice outputs.
   >  --title 'Real-time tracking of Zika virus evolution -- v2 JSON' \
   >  --panels tree map entropy frequencies > /dev/null
 
-  $ augur validate export-v2 "$TMP/out/v2_zika.json" > /dev/null
+  $ ../../../bin/augur validate export-v2 "$TMP/out/v2_zika.json" > /dev/null
 
 Switch back to the original directory where testing started.