diff test-data/MADE1.nhmmscan_out @ 5:b2453ee52845 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
author iuc
date Tue, 16 Jun 2020 05:29:04 -0400
parents ca0b674e895b
children 24fa8e890f08
line wrap: on
line diff
--- a/test-data/MADE1.nhmmscan_out	Mon Jun 11 15:51:03 2018 -0400
+++ b/test-data/MADE1.nhmmscan_out	Tue Jun 16 05:29:04 2020 -0400
@@ -1,12 +1,12 @@
 # nhmmscan :: search DNA sequence(s) against a DNA profile database
-# HMMER 3.2 (June 2018); http://hmmer.org/
-# Copyright (C) 2018 Howard Hughes Medical Institute.
+# HMMER 3.3 (Nov 2019); http://hmmer.org/
+# Copyright (C) 2019 Howard Hughes Medical Institute.
 # Freely distributed under the BSD open source license.
 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
-# query sequence file:             /tmp/tmpp4O0Ju/files/000/dataset_41.dat
+# query sequence file:             /tmp/tmpqydies2m/files/f/a/5/dataset_fa559c91-0436-48cb-a47d-20062d4af284.dat
 # target HMM database:             localref.hmm
-# per-seq hits tabular output:     /tmp/tmpp4O0Ju/files/000/dataset_43.dat
-# hits output in Dfam format:      /tmp/tmpp4O0Ju/files/000/dataset_44.dat
+# per-seq hits tabular output:     /tmp/tmpqydies2m/files/4/7/2/dataset_4723128d-8711-4edb-8afe-a68476a6c127.dat
+# hits output in Dfam format:      /tmp/tmpqydies2m/files/1/a/e/dataset_1aeea50b-1263-4750-8237-4fc3f10c0999.dat
 # max ASCII text line length:      unlimited
 # Vit filter P threshold:       <= 0.001
 # Fwd filter P threshold:       <= 1e-05
@@ -18,79 +18,79 @@
 Scores for complete hit:
     E-value  score  bias  Model     start    end  Description
     ------- ------ -----  --------  -----  -----  -----------
-    8.7e-11   39.2   7.4  MADE1    302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
-    6.4e-08   30.0   8.3  MADE1    174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
-    9.3e-08   29.5   6.1  MADE1    302466 302390 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
-    6.3e-06   23.7   7.0  MADE1    174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+      4e-11   41.3   7.5  MADE1    302390 302466 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+    1.9e-08   32.8   8.3  MADE1    174456 174498 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+    6.3e-08   31.0   6.7  MADE1    302466 302389 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+    4.9e-06   25.0   7.0  MADE1    174493 174456 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
   ------ inclusion threshold ------
-        1.4    6.5   7.0  MADE1    304073 304104 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
+        2.2    6.9   7.2  MADE1    304073 304103 MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
 
 
 Annotation for each hit  (and alignments):
 >> MADE1  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to      mod len      acc
    ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
- !   39.2   7.4   8.7e-11         4        80 .]    302390    302466 ..    302387    302466 ..        80    0.87
+ !   41.3   7.5     4e-11         4        80 .]    302390    302466 ..    302387    302466 ..        80    0.88
 
   Alignment:
-  score: 39.2 bits
+  score: 41.3 bits
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MADE1      4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80    
-                                       ggt ggtgcaaaa  aattg ggtttttgccatt cttttaat gc    a aaa  g  a t ctttt caccaa ctaa
-  humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttA-AAA--GT-AATGCTTTTACACCAATCTAA 302466
-                                       899******************************************955533.443..33.44689************9986 PP
+                                       ggt ggtgcaaaa  aattg ggtttttgccatt cttttaat gc    aaaa   g  a t ctttt caccaa ctaa
+  humanchr1/239220001-239550000 302390 GGTCGGTGCAAAATCAATTGTGGTTTTTGCCATTGCTTTTAATTGCttttAAAA---GT-AATGCTTTTACACCAATCTAA 302466
+                                       89*******************************************966644554...34.4578**************997 PP
 
 >> MADE1  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to      mod len      acc
    ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
- !   30.0   8.3   6.4e-08         1        43 [.    174456    174498 ..    174456    174518 ..        80    0.92
+ !   32.8   8.3   1.9e-08         1        43 [.    174456    174498 ..    174456    174518 ..        80    0.91
 
   Alignment:
-  score: 30.0 bits
+  score: 32.8 bits
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MADE1      1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43    
                                        ttaggtt gtgcaaaagtaattg ggtttttg cattactttt
   humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
-                                       589************************************9975 PP
+                                       589************************************9986 PP
 
 >> MADE1  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to      mod len      acc
    ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
- !   29.5   6.1   9.3e-08         1        77 [.    302466    302390 ..    302466    302387 ..        80    0.74
+ !   31.0   6.7   6.3e-08         1        78 [.    302466    302389 ..    302466    302387 ..        80    0.80
 
   Alignment:
-  score: 29.5 bits
-                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx................xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
-                          MADE1      1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt................aatggcaaaaaccgcaattacttttgcaccaacc 77    
-                                       ttag ttggtg aaaag                cattactttt                aatggcaaaaacc caatt  ttttgcacc acc
-  humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAG----------------CATTACTTTTaaaagcaattaaaagcAATGGCAAAAACCACAATTGATTTTGCACCGACC 302390
-                                       68999999999999998................4666777765222222222222222268****************************9998 PP
+  score: 31.0 bits
+                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+                          MADE1      1 ttaggttggtgcaaaagtaattgcggttttt....gccattacttttaatggcaaaaaccgcaattacttttgcaccaacct 78    
+                                       ttag ttggtg aaaag a t      tttt    gc atta    +aatggcaaaaacc caatt  ttttgcacc acc 
+  humanchr1/239220001-239550000 302466 TTAGATTGGTGTAAAAGCATT-A---CTTTTaaaaGCAATTAAAAGCAATGGCAAAAACCACAATTGATTTTGCACCGACCA 302389
+                                       6899************97543.2...23333455566666666666799*****************************9985 PP
 
 >> MADE1  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to      mod len      acc
    ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
- !   23.7   7.0   6.3e-06        43        80 .]    174493    174456 ..    174513    174456 ..        80    0.91
+ !   25.0   7.0   4.9e-06        43        80 .]    174493    174456 ..    174513    174456 ..        80    0.94
 
   Alignment:
-  score: 23.7 bits
+  score: 25.0 bits
                                        xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                           MADE1     43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80    
                                        taatg caaaaacc caattacttttgcac aacctaa
   humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456
-                                       689********************************986 PP
+                                       5899*******************************986 PP
 
 >> MADE1  MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
     score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to      mod len      acc
    ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
- ?    6.5   7.0       1.4        41        72 ..    304073    304104 ..    304053    304109 ..        80    0.85
+ ?    6.9   7.2       2.2        41        71 ..    304073    304103 ..    304053    304109 ..        80    0.85
 
   Alignment:
-  score: 6.5 bits
-                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
-                          MADE1     41 tttaatggcaaaaaccgcaattacttttgcac 72    
-                                       tt a tgg aaaaa   ca tta ttttgca 
-  humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCAT 304104
-                                       455779************************86 PP
+  score: 6.9 bits
+                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
+                          MADE1     41 tttaatggcaaaaaccgcaattacttttgca 71    
+                                       tt a tgg aaaaa   ca tta ttttgca
+  humanchr1/239220001-239550000 304073 TTAAGTGGGAAAAAATACACTTATTTTTGCA 304103
+                                       456789************************8 PP
 
 
 
@@ -98,12 +98,12 @@
 -------------------------------------
 Query sequence(s):                         1  (660000 residues searched)
 Target model(s):                           1  (80 nodes)
-Residues passing SSV filter:           63737  (0.0966); expected (0.02)
-Residues passing bias filter:          44695  (0.0677); expected (0.02)
-Residues passing Vit filter:            2309  (0.0035); expected (0.001)
-Residues passing Fwd filter:            2041  (0.00309); expected (1e-05)
+Residues passing SSV filter:           60770  (0.0921); expected (0.02)
+Residues passing bias filter:          35792  (0.0542); expected (0.02)
+Residues passing Vit filter:            1612  (0.00244); expected (0.001)
+Residues passing Fwd filter:            1194  (0.00181); expected (1e-05)
 Total number of hits:                      5  (0.000405)
 # CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
-# Mc/sec: 2407.09
+# Mc/sec: 2289.06
 //
 [ok]