diff test-data/files/align.log.2 @ 0:9a3a2e04f47a draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/files/align.log.2	Mon Jun 10 16:04:10 2019 -0400
@@ -0,0 +1,65 @@
+inputfile = orig
+3 x 70 - 70 d
+outputhat23=1
+treein = 0
+compacttree = 0
+stacksize: 8192 kb
+generating a scoring matrix for nucleotide (dist=200) ... done
+All-to-all alignment.
+    0 / 3 (by thread   0) 
tbfast-pair (nuc) Version 7.407
+alg=L, model=DNA200 (2), 2.00 (6.00), -0.10 (-0.30), noshift, amax=0.0
+1 thread(s)
+
+outputhat23=1
+Loading 'hat3.seed' ... 
+done.
+Writing hat3 for iterative refinement
+generating a scoring matrix for nucleotide (dist=200) ... done
+Gap Penalty = -1.53, +0.00, +0.00
+tbutree = 1, compacttree = 0
+Constructing a UPGMA tree ... 
+
    0 / 3
+done.
+
+Progressive alignment ... 
+
STEP     1 /2 (thread    0) 
+Reallocating (by thread 0) ..done. *alloclen = 1142
+
STEP     2 /2 (thread    0) 
+done.
+tbfast (nuc) Version 7.407
+alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
+1 thread(s)
+
+minimumweight = 0.000010
+autosubalignment = 0.000000
+nthread = 1
+randomseed = 0
+blosum 62 / kimura 200
+poffset = 0
+niter = 1
+sueff_global = 0.100000
+nadd = 1
+Loading 'hat3' ... done.
+generating a scoring matrix for nucleotide (dist=200) ... done
+
+
    0 / 3
+Segment   1/  1    1-  84
+001-0000-0 (thread    1) identical     
001-0000-0 (thread    1) better     

001-0001-1 (thread    1) identical     

001-0002-1 (thread    1) identical     
001-0002-1 (thread    1) worse      
+Reached 1
+done
+dvtditr (nuc) Version 7.407
+alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
+1 thread(s)
+
+
+Strategy:
+ L-INS-i (Probably most accurate, very slow)
+ Iterative refinement method (<1) with LOCAL pairwise alignment information
+
+If unsure which option to use, try 'mafft --auto input > output'.
+For more information, see 'mafft --help', 'mafft --man' and the mafft page.
+
+The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
+It tends to insert more gaps into gap-rich regions than previous versions.
+To disable this change, add the --leavegappyregion option.
+