Mercurial > repos > dfornika > augur
diff test-data/output.log @ 1:892c6690a1e8 draft default tip
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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.log Mon Apr 08 13:27:08 2019 -0400 @@ -0,0 +1,52 @@ +inputfile = orig +5 x 8 - 7 d +nthread = 1 +nthreadpair = 1 +nthreadtb = 1 +ppenalty_ex = 0 +stacksize: 8192 kb +generating a scoring matrix for nucleotide (dist=200) ... done +Gap Penalty = -1.53, +0.00, +0.00 + + + +Making a distance matrix .. + 1 / 5 (thread 0) +done. + +Constructing a UPGMA tree (efffree=0) ... + 0 / 5 +done. + +Progressive alignment 1/2... + STEP 1 / 4 (thread 0) f STEP 2 / 4 (thread 0) d STEP 3 / 4 (thread 0) d STEP 4 / 4 (thread 0) d +done. + +Making a distance matrix from msa.. + 0 / 5 (thread 0) +done. + +Constructing a UPGMA tree (efffree=1) ... + 0 / 5 +done. + +Progressive alignment 2/2... + STEP 1 / 4 (thread 0) f STEP 2 / 4 (thread 0) d STEP 3 / 4 (thread 0) d STEP 4 / 4 (thread 0) d +done. + +disttbfast (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: + FFT-NS-2 (Fast but rough) + Progressive method (guide trees were built 2 times.) + +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. +