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Welcome to the BaitFisher program, version 1.2.6
This software and any of its components are copyright protected by the authors
Christoph Mayer and Oliver Niehuis, Zoologisches Forschungsmuseum Alexander
Koenig, Bonn, Germany. Copyright 2014.
This software is distributed as working material within a workshop given by
Manuela Sann and Oliver Niehuis at the Australian National University, Canberra.
As long as it is not published, the software may only be used for the purposes of
the workshop or with explicit permission of one of the authors.
Redistribution as source code in part or in whole or in binary form is not permitted.
The software comes without warranty of any kind.
PROGRAM has been started with the following parameters:
Alignment cutting yes
Name of gff file: Nvit-genome/Nvit_OGSv1.2_reduced.gff2
Name of genome file: Nvit-genome/Nvit_1.0_scaffolds_reduced.fa
Name of genome: Nasonia_vitripennis
GFF feature to be excised from sequences: CDS
GFF record attribute name for geneID: GenePrediction
String with required taxonomic groups: (Podalonia_hirsuta),(Isodontia_mexicana,Prionyx_kirbii,Sphex_funerarius),(Sceliphron_curvatum,Chalybion_californicum),(Dinetus_pictus),(Alysson_spinosus),(Nysson_niger),(Gorytes_laticinctus,Harpactus_elegans,Sphecius_convallis),(Stizoides_tridentatus),(Bembix_rostrata),(Oxybelus_bipunctatus),(Crabro_peltarius,Crossocerus_quadrimaculatus),(Philanthus_triangulum),(Cerceris_arenaria),(Tachysphex_fulvitarsis),(Trypoxylon_figulus),(Diodontus_minutus,Pemphredon_lugens),(Psenulus_fuscipennis)
Name of directory with transcriptome files: alignments
Cluster threshold: 0.15
Bait length: 120
Bait offset (for multiple baits in region): 20
Bait number (for multiple baits in region): 3
Output directory: BaitFisher-results
Remove refernce species from alignment: yes
sequence_name_field_delimiter (default "|") |
Number of taxon field in sequence name: 3
Number of geneID field in sequence name: 4
Center computation mode: heuristic
Verbosity: 5
INFORMATION: Could not find the file with alignment parameters: simpledna_N0.mat
The following default values will be assumed as alignment parameters:
Gap openening penalty: 0
Gap extension penalty: -3
Match score: 1
Mismatch score: -2
Score against N: 0
Scores against other ambigs: match or mismatch score
Parsing the gff file ... Done.
Reading the genome file ...Done.
PROGRESS: 2017-06-07 13:35:56 Genome file has been read.
PROGRESS: 2017-06-07 13:35:56 Reading alignemnt file (1/5): alignments/EOG5B2RVS.linsi.nt_without_bees_ants_rmgo.fas
PROGRESS: Working with gene: NV16710-RA 1/7 found in genome at SCAFFOLD42 1871783 1871919
NOTICE: Skipping CDS feature alignment in NV16710-RA with number 1/7 in NV16710-RA since it is too short. Alignment length: 137. Minimum length: 160
PROGRESS: Working with gene: NV16710-RA 2/7 found in genome at SCAFFOLD42 1872301 1872892
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 39%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 49%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 59%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 69%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 79%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 89%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 99%.
PROGRESS: Working with gene: NV16710-RA 3/7 found in genome at SCAFFOLD42 1872965 1873300
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 38%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 48%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 58%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 68%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 77%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 87%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 97%.
PROGRESS: Working with gene: NV16710-RA 4/7 found in genome at SCAFFOLD42 1873377 1873442
NOTICE: Skipping CDS feature alignment in NV16710-RA with number 4/7 in NV16710-RA since it is too short. Alignment length: 66. Minimum length: 160
PROGRESS: Working with gene: NV16710-RA 5/7 found in genome at SCAFFOLD42 1873527 1873749
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 38%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 48%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 58%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 67%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 77%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 87%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 97%.
PROGRESS: Working with gene: NV16710-RA 6/7 found in genome at SCAFFOLD42 1873834 1874002
ALERT: No valid bait regions found for feature: NV16710-RA 6/7
PROGRESS: Working with gene: NV16710-RA 7/7 found in genome at SCAFFOLD42 1874080 1874149
NOTICE: Skipping CDS feature alignment in NV16710-RA with number 7/7 in NV16710-RA since it is too short. Alignment length: 70. Minimum length: 160
NOTE: Alignment contains 7 features, of which 3 have at least one valid bait region.
PROGRESS: 2017-06-07 13:35:57 Reading alignemnt file (2/5): alignments/EOG5B2RVT.linsi.nt_without_bees_ants_rmgo.fas
PROGRESS: Working with gene: NV18410-RA 1/6 found in genome at SCAFFOLD188 48838 48923
NOTICE: Skipping CDS feature alignment in NV18410-RA with number 1/6 in NV18410-RA since it is too short. Alignment length: 86. Minimum length: 160
PROGRESS: Working with gene: NV18410-RA 2/6 found in genome at SCAFFOLD188 49006 49464
ALERT: No valid bait regions found for feature: NV18410-RA 2/6
PROGRESS: Working with gene: NV18410-RA 3/6 found in genome at SCAFFOLD188 49558 49788
ALERT: No valid bait regions found for feature: NV18410-RA 3/6
PROGRESS: Working with gene: NV18410-RA 4/6 found in genome at SCAFFOLD188 50604 50888
ALERT: No valid bait regions found for feature: NV18410-RA 4/6
PROGRESS: Working with gene: NV18410-RA 5/6 found in genome at SCAFFOLD188 50966 51131
ALERT: No valid bait regions found for feature: NV18410-RA 5/6
PROGRESS: Working with gene: NV18410-RA 6/6 found in genome at SCAFFOLD188 51214 51363
NOTICE: Skipping CDS feature alignment in NV18410-RA with number 6/6 in NV18410-RA since it is too short. Alignment length: 150. Minimum length: 160
ALERT: Alignment contains 6 features but no single valid bait region. (Details: see above.)
PROGRESS: 2017-06-07 13:35:57 Reading alignemnt file (3/5): alignments/EOG5ZPCSX.linsi.nt_without_bees_ants_rmgo.fas
PROGRESS: Working with gene: NV13708-RA 1/3 found in genome at SCAFFOLD14 3092403 3092478
NOTICE: Skipping CDS feature alignment in NV13708-RA with number 1/3 in NV13708-RA since it is too short. Alignment length: 76. Minimum length: 160
PROGRESS: Working with gene: NV13708-RA 2/3 found in genome at SCAFFOLD14 3092626 3092963
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:57 Percent done this alignment or gene: 38%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 48%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 58%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 67%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 77%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 87%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 96%.
PROGRESS: Working with gene: NV13708-RA 3/3 found in genome at SCAFFOLD14 3093079 3094365
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 39%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 49%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 59%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 69%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 79%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 89%.
PROGRESS: 2017-06-07 13:35:58 Percent done this alignment or gene: 99%.
NOTE: Alignment contains 3 features, of which 2 have at least one valid bait region.
PROGRESS: 2017-06-07 13:35:59 Reading alignemnt file (4/5): alignments/EOG5ZPCT0.linsi.nt_without_bees_ants_rmgo.fas
PROGRESS: Working with gene: NV11525-RA 1/2 found in genome at SCAFFOLD4 3975384 3976592
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 39%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 49%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 59%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 69%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 79%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 89%.
PROGRESS: 2017-06-07 13:35:59 Percent done this alignment or gene: 99%.
PROGRESS: Working with gene: NV11525-RA 2/2 found in genome at SCAFFOLD4 3977689 3977706
NOTICE: Skipping CDS feature alignment in NV11525-RA with number 2/2 in NV11525-RA since it is too short. Alignment length: 18. Minimum length: 160
NOTE: Alignment contains 2 features, of which 1 have at least one valid bait region.
PROGRESS: 2017-06-07 13:35:59 Reading alignemnt file (5/5): alignments/EOG5ZW48P.linsi.nt_without_bees_ants_rmgo.fas
PROGRESS: Working with gene: NV13720-RA 1/12 found in genome at SCAFFOLD14 3243871 3244028
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 1/12 in NV13720-RA since it is too short. Alignment length: 158. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 2/12 found in genome at SCAFFOLD14 3245535 3245701
ALERT: No valid bait regions found for feature: NV13720-RA 2/12
PROGRESS: Working with gene: NV13720-RA 3/12 found in genome at SCAFFOLD14 3254088 3254228
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 3/12 in NV13720-RA since it is too short. Alignment length: 141. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 4/12 found in genome at SCAFFOLD14 3269767 3270109
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 9%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 19%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 29%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 39%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 49%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 59%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 69%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 78%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 88%.
PROGRESS: 2017-06-07 13:36:00 Percent done this alignment or gene: 98%.
PROGRESS: Working with gene: NV13720-RA 5/12 found in genome at SCAFFOLD14 3270634 3270758
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 5/12 in NV13720-RA since it is too short. Alignment length: 125. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 6/12 found in genome at SCAFFOLD14 3270843 3271110
ALERT: No valid bait regions found for feature: NV13720-RA 6/12
PROGRESS: Working with gene: NV13720-RA 7/12 found in genome at SCAFFOLD14 3271211 3271402
ALERT: No valid bait regions found for feature: NV13720-RA 7/12
PROGRESS: Working with gene: NV13720-RA 8/12 found in genome at SCAFFOLD14 3271481 3271624
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 8/12 in NV13720-RA since it is too short. Alignment length: 144. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 9/12 found in genome at SCAFFOLD14 3271814 3271910
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 9/12 in NV13720-RA since it is too short. Alignment length: 97. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 10/12 found in genome at SCAFFOLD14 3271989 3272147
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 10/12 in NV13720-RA since it is too short. Alignment length: 159. Minimum length: 160
PROGRESS: Working with gene: NV13720-RA 11/12 found in genome at SCAFFOLD14 3273982 3274458
ALERT: No valid bait regions found for feature: NV13720-RA 11/12
PROGRESS: Working with gene: NV13720-RA 12/12 found in genome at SCAFFOLD14 3276550 3276609
NOTICE: Skipping CDS feature alignment in NV13720-RA with number 12/12 in NV13720-RA since it is too short. Alignment length: 60. Minimum length: 160
NOTE: Alignment contains 12 features, of which 1 have at least one valid bait region.
PROGRESS: Bait-Fisher handled 5 alignment files.
Bait-Fisher finished without errors.
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