Mercurial > repos > dfornika > augur

comparison test-data/output.log @ 1:892c6690a1e8 draft default tip

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/tools/augur commit a71ecf1b4a86227084935c6f60dfd130b7d0997b-dirty
author dfornika
date Mon, 08 Apr 2019 13:27:08 -0400
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0:20ad934c5536 1:892c6690a1e8
1 inputfile = orig
2 5 x 8 - 7 d
3 nthread = 1
4 nthreadpair = 1
5 nthreadtb = 1
6 ppenalty_ex = 0
7 stacksize: 8192 kb
8 generating a scoring matrix for nucleotide (dist=200) ... done
9 Gap Penalty = -1.53, +0.00, +0.00
10
11
12
13 Making a distance matrix ..
14
15 1 / 5 (thread 0)
16 done.
17
18 Constructing a UPGMA tree (efffree=0) ...
19
20 0 / 5
21 done.
22
23 Progressive alignment 1/2...
24
25 STEP 1 / 4 (thread 0) f
26 STEP 2 / 4 (thread 0) d
27 STEP 3 / 4 (thread 0) d
28 STEP 4 / 4 (thread 0) d
29 done.
30
31 Making a distance matrix from msa..
32
33 0 / 5 (thread 0)
34 done.
35
36 Constructing a UPGMA tree (efffree=1) ...
37
38 0 / 5
39 done.
40
41 Progressive alignment 2/2...
42
43 STEP 1 / 4 (thread 0) f
44 STEP 2 / 4 (thread 0) d
45 STEP 3 / 4 (thread 0) d
46 STEP 4 / 4 (thread 0) d
47 done.
48
49 disttbfast (nuc) Version 7.407
50 alg=A, model=DNA200 (2), 1.53 (4.59), -0.00 (-0.00), noshift, amax=0.0
51 1 thread(s)
52
53
54 Strategy:
55 FFT-NS-2 (Fast but rough)
56 Progressive method (guide trees were built 2 times.)
57
58 If unsure which option to use, try 'mafft --auto input > output'.
59 For more information, see 'mafft --help', 'mafft --man' and the mafft page.
60
61 The default gap scoring scheme has been changed in version 7.110 (2013 Oct).
62 It tends to insert more gaps into gap-rich regions than previous versions.
63 To disable this change, add the --leavegappyregion option.
64