annotate test-data/nhmmer.out @ 5:b4fe2f703b4b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"

# nhmmer :: search a DNA model, alignment, or sequence against a DNA database
# HMMER 3.3 (Nov 2019); http://hmmer.org/
# Copyright (C) 2019 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query file:                      /tmp/tmpqydies2m/files/c/4/e/dataset_c4e67f40-cb86-438e-8bc0-6020ada9fc86.dat
# target sequence database:        /tmp/tmpqydies2m/files/a/1/b/dataset_a1b4364c-0e9a-4709-b4ef-ab7e5661d9e9.dat
# hits tabular output:             /tmp/tmpqydies2m/files/b/d/d/dataset_bdd87d82-1ce1-4051-8d5f-f7251bf7fd18.dat
# hits output in Dfam format:      /tmp/tmpqydies2m/files/d/8/e/dataset_d8ee0d50-d171-4e8a-9c7d-1cbd4394296f.dat
# alignment scores output:         /tmp/tmpqydies2m/files/5/1/3/dataset_5139892f-c507-40c4-b43d-f73023c634f4.dat
# max ASCII text line length:      unlimited
# SSV filter P threshold:       <= 0.02
# Vit filter P threshold:       <= 0.001
# Fwd filter P threshold:       <= 1e-05
# input query is asserted as:      DNA
# random number seed set to:       4
# number of worker threads:        1
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       MADE1  [M=80]
Accession:   DF0000629.2
Description: MADE1 (MAriner Derived Element 1), a TcMar-Mariner DNA transposon
Scores for complete hits:
    E-value  score  bias  Sequence                       start    end  Description
    ------- ------ -----  --------                       -----  -----  -----------
      4e-11   41.3   7.5  humanchr1/239220001-239550000 302390 302466 
    1.9e-08   32.8   8.3  humanchr1/239220001-239550000 174456 174498 
    6.3e-08   31.0   6.7  humanchr1/239220001-239550000 302466 302389 
    4.9e-06   25.0   7.0  humanchr1/239220001-239550000 174493 174456 
  ------ inclusion threshold ------
        2.2    6.9   7.2  humanchr1/239220001-239550000 304073 304103 


Annotation for each hit  (and alignments):
>> humanchr1/239220001-239550000  
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to       sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
 !   41.3   7.5     4e-11         4        80 .]    302390    302466 ..    302387    302466 ..    330000    0.88

  Alignment:
  score: 41.3 bits
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx....xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MADE1      4 ggttggtgcaaaagtaattgcggtttttgccattacttttaatggc....aaaaaccgcaattacttttgcaccaacctaa 80    
                                       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

>> humanchr1/239220001-239550000  
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to       sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
 !   32.8   8.3   1.9e-08         1        43 [.    174456    174498 ..    174456    174518 ..    330000    0.91

  Alignment:
  score: 32.8 bits
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MADE1      1 ttaggttggtgcaaaagtaattgcggtttttgccattactttt 43    
                                       ttaggtt gtgcaaaagtaattg ggtttttg cattactttt
  humanchr1/239220001-239550000 174456 TTAGGTTAGTGCAAAAGTAATTGTGGTTTTTGTCATTACTTTT 174498
                                       589************************************9986 PP

>> humanchr1/239220001-239550000  
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to       sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
 !   31.0   6.7   6.3e-08         1        78 [.    302466    302389 ..    302466    302387 ..    330000    0.80

  Alignment:
  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

>> humanchr1/239220001-239550000  
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to       sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
 !   25.0   7.0   4.9e-06        43        80 .]    174493    174456 ..    174513    174456 ..    330000    0.94

  Alignment:
  score: 25.0 bits
                                       xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx RF
                          MADE1     43 taatggcaaaaaccgcaattacttttgcaccaacctaa 80    
                                       taatg caaaaacc caattacttttgcac aacctaa
  humanchr1/239220001-239550000 174493 TAATGACAAAAACCACAATTACTTTTGCACTAACCTAA 174456
                                       5899*******************************986 PP

>> humanchr1/239220001-239550000  
    score  bias    Evalue   hmmfrom    hmm to     alifrom    ali to      envfrom    env to       sq len      acc
   ------ ----- ---------   -------   -------    --------- ---------    --------- ---------    ---------    ----
 ?    6.9   7.2       2.2        41        71 ..    304073    304103 ..    304053    304109 ..    330000    0.85

  Alignment:
  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



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (80 nodes)
Target sequences:                          1  (660000 residues searched)
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: 0.04u 0.00s 00:00:00.04 Elapsed: 00:00:00.05
# Mc/sec: 1031.54
//
[ok]