Commit 2f3dd7b4 authored by Mathieu's avatar Mathieu

BUSCO 3.0.0

parent 89aa1ab2
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3.0.0
- Major refactoring of the code
- Introduce setup.py
- Introduce the config.ini file
- Issue #24 fixed
- Issue #25 fixed
- Switch to the MIT License
2.0.1
- Stop the execution when tblastn crashes, instead of just warning the user
- Issue #16 fixed
......
File mode changed from 100644 to 100755
This diff is collapsed.
**BUSCO - Benchmarking sets of Universal Single-Copy Orthologs.**
To get help, ``python BUSCO.py -h`` and ``python BUSCO_plot.py -h``.
To get help, ``python scripts/run_BUSCO.py -h`` and ``python scripts/generate_plot.py -h``
See also the user guide: BUSCO_v2.0_userguide.pdf
See also the user guide: BUSCO_v3_userguide.pdf
You can download BUSCO datasets on http://busco.ezlab.org
*Copyright (C) 2016 E. Zdobnov lab*
BUSCO is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version. See <http://www.gnu.org/licenses/>
BUSCO is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
Copyright (c) 2016-2017, Evgeny Zdobnov ([email protected])
Licensed under the MIT license. See LICENSE.md file.
## BUSCO specific configuration
## It overrides default values in code and dataset cfg, and is overridden by arguments in command line
## Uncomment lines with single # when appropriate
[busco]
## Input file
# in = ./sample_data/target.fa
## Run name, used in output files and folder
# out = SAMPLE
## Where to store the output directory
# out_path = ./sample_data
## Path to the BUSCO dataset
# lineage_path = ./sample_data/example
## Which mode to run (genome / protein / transcriptome)
# mode = genome
## How many threads to use for multithreaded steps
# cpu = 1
## Domain for augustus retraining, eukaryota or prokaryota
# domain = eukaryota # do not change this unless you know exaclty why !!!
## Force rewrite if files already exist (True/False)
# force = False
## Restart mode (True/False)
# restart = False
## Blast e-value
# evalue = 1e-3
## Species to use with augustus, for old datasets only
# species = fly
## Augustus extra parameters
# augustus_parameters = '' # nothing here, use single quotes, like this: '--param1=1 --param2=2'
## Tmp folder
# tmp_path = ./tmp/
## How many candidate regions (contigs, scaffolds) to consider for each BUSCO
# limit = 3
## Augustus long mode for retraining (True/False)
# long = False
## Quiet mode (True/False)
# quiet = False
## Debug logs (True/False), it needs Quiet to be False
# debug = True
## tar gzip output files (True/False)
# gzip = False
[tblastn]
## path to tblastn
path = /usr/bin/
[makeblastdb]
## path to makeblastdb
path = /usr/bin/
[augustus]
## path to augustus
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/
[etraining]
## path to augustus etraining
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/
## path to augustus perl scripts, redeclare it for each new script
[gff2gbSmallDNA.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/
[new_species.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/
[optimize_augustus.pl]
path = /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/scripts/
[hmmsearch]
## path to HMMsearch executable
path = /home/osboxes/BUSCOVM/hmmer/hmmer-3.1b2-linux-intel-ia32/binaries/
[Rscript]
## path to Rscript, if you wish to use the plot tool
path = /usr/bin/
Warning: Block unknown_C is not significant enough, removed from profile.
Warning: Block unknown_D is not significant enough, removed from profile.
Warning: Block unknown_G is not significant enough, removed from profile.
Warning: Block unknown_A is not significant enough, removed from profile.
Warning: Block unknown_B is not significant enough, removed from profile.
Warning: Block unknown_C is not significant enough, removed from profile.
Will create parameters for a EUKARYOTIC species!
creating directory /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/ ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_parameters.cfg ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_weightmatrix.txt ...
creating /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_metapars.cfg ...
The necessary files for training BUSCO_SAMPLE_1214242381 have been created.
Now, either run etraining or optimize_parameters.pl with --species=BUSCO_SAMPLE_1214242381.
creating directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/species/BUSCO_SAMPLE_1279401836/ ...
creating /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/species/BUSCO_SAMPLE_1279401836/BUSCO_SAMPLE_1279401836_parameters.cfg ...
creating /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/species/BUSCO_SAMPLE_1279401836/BUSCO_SAMPLE_1279401836_weightmatrix.txt ...
creating /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/species/BUSCO_SAMPLE_1279401836/BUSCO_SAMPLE_1279401836_metapars.cfg ...
The necessary files for training BUSCO_SAMPLE_1279401836 have been created.
Now, either run etraining or optimize_parameters.pl with --species=BUSCO_SAMPLE_1279401836.
etraining quickly estimates the parameters from a file with training genes.
optimize_augustus.pl alternates running etraining and augustus to find optimal metaparameters.
......@@ -29,7 +29,8 @@ Quantiles of the GC contents in the training set:
HMM-training the parameters...
i= 0 bc= (0.237, 0.263, 0.263, 0.237)
** building model for exons *EXON*
tis bin boundaries
start codon frequencies: ATG(8)
# admissible start codons and their probabilities: ATG(1), CTG(0), TTG(0)
number of bases in the reading frames: 2806 2814 2814
--- frame = 0 --- minPatSum = 233
--- frame = 1 --- minPatSum = 233
......@@ -56,4 +57,4 @@ taa: 3 (0.375)
tga: 1 (0.125)
end *EXON*
Storing parameters to file...
Writing exon model parameters [1] to file /home/xxx/augustus-3.2.2/config/species/BUSCO_SAMPLE_1214242381/BUSCO_SAMPLE_1214242381_exon_probs.pbl.
Writing exon model parameters [1] to file /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/species/BUSCO_SAMPLE_1279401836/BUSCO_SAMPLE_1279401836_exon_probs.pbl.
......@@ -3,12 +3,12 @@ sample AUGUSTUS transcript 62761 68675 0.22 + . g1.t1
sample AUGUSTUS exon 62761 63926 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 66254 66359 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 66312 66314 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.5 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.46 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.51 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.51 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.93 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.78 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 67338 67542 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.49 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.88 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
......
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[0..111]--> unknown_A (17) <--[0..101]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10482, name = sample) -----
......@@ -108,6 +108,7 @@ sample AUGUSTUS protein_match 30543 30588 8.96 - 0 target "unknown_A[1..16]"; ta
# protein sequence = [MSRNLFLSITNLFRNLESLFLPHGGHPPALALAGFQHDHSHRSSQEFSLKQLIGDGMLWAVPKHRRSVEKRLKRKFGY
# PEYNWKPLREKRNIRSCLQCGHDHEMGVLCPFCYQKVLKETELMQSKIQETLGLDPVDKEVIVLYEGEKAEQSSDELKNKRIVEMKKPRPMWFTKNLL
# QKSTQQLSETKEVKPSDLA]
# sequence of block unknown_A 93 [SCLQCGHDHEMGVLCPF] 110
# end gene g3
###
# start gene g4
......@@ -127,4 +128,4 @@ sample AUGUSTUS tts 32490 32490 . + . transcript_id "g4.t1"; gene_id "g4";
# end gene g4
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_1.prfl --predictionStart=25227 --predictionEnd=35708 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_1.prfl --predictionStart=25227 --predictionEnd=35708 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[0..348]--> unknown_A (44) <--[0..8]--> unknown_B (36) <--[0..13]--> unknown_C (16) <--[1..27]--> unknown_D (73) <--[0..15]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 24405, name = sample) -----
......@@ -162,6 +162,10 @@ sample AUGUSTUS protein_match 46207 46425 9.82 + 0 target "unknown_D[1..73]"; ta
# HQLVHKQRQIALFSEMVHSASLVHDDVIDQSDFRRGKPSVNALWNHKKVTMAGDYILSIASIMIARLRSDDVTIVLSQILTDLVQGEFMQLGSRETEN
# ERFAHYLTKTYRKTASLIANALKATAVIAQADDNVAEVAFQYGRNIGLAFQLVDDMLDFVSSTEQMGKPTAADLKLGLATAPVLFACEKYPELNPMVM
# RRFSEPGDVERAFELVHKSHGLEQTRFLAKKHCNEAIRLAQELTESPYQKGLQVVADLVINRMK]
# sequence of block unknown_A 254 [ILTDLVQGEFMQLGSRETENERFAHYLTKTYRKTASLIANALKA] 298
# sequence of block unknown_B 298 [TAVIAQADDNVAEVAFQYGRNIGLAFQLVDDMLDFV] 334
# sequence of block unknown_C 346 [DLKLGLATAPVLFACE] 362
# sequence of block unknown_D 363 [YPELNPMVMRRFSEPGDVERAFELVHKSHGLEQTRFLAKKHCNEAIRLAQELTESPYQKGLQVVADLVINRMK] 436
# end gene g4
###
# start gene g5
......@@ -204,4 +208,4 @@ sample AUGUSTUS exon 50924 51425 . + . transcript_id "g5.t1"; gene_id "g5";
# end gene g5
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_2.prfl --predictionStart=27021 --predictionEnd=51425 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_2.prfl --predictionStart=27021 --predictionEnd=51425 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[15..26]--> unknown_C (6) <--[15..40]--> unknown_D (32) <--[1..45]--> unknown_E (13) <--[0..2]--> unknown_F (28) <--[0..6]--> unknown_G (9) <--[3..810]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10906, name = sample) -----
......@@ -20,12 +20,12 @@ sample AUGUSTUS transcript 62761 68675 0.22 + . g1.t1
sample AUGUSTUS exon 62761 63926 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 66254 66359 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 66312 66314 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.5 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.46 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.51 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.51 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.93 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.78 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 67338 67542 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.49 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.88 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
......@@ -41,6 +41,11 @@ sample AUGUSTUS protein_match 68259 68285 12.5 + 0 target "unknown_G[1..9]"; tar
# tgttctgtttgatgatggccttcctgctgttgttcgccttctaa]
# protein sequence = [MFVSTVSRIAPVARSAFLANSKQYLRPLSSAIISQSQTLAAQNTTPVALLPQIRSFQTSPVTRDIDSAAKFIGAGAAT
# VGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAMGLFCLMMAFLLLFAF]
# sequence of block unknown_C 24 [LRPLSS] 30
# sequence of block unknown_D 52 [IRSFQTSPVTRDIDSAAKFIGAGAATVGVAGS] 84
# sequence of block unknown_E 85 [AGIGTVFGSLIIG] 98
# sequence of block unknown_F 98 [YARNPSLKQQLFSYAILGFALSEAMGLF] 126
# sequence of block unknown_G 126 [CLMMAFLLL] 135
# end gene g1
###
# start gene g2
......@@ -120,4 +125,4 @@ sample AUGUSTUS CDS 72676 73243 0.97 + 0 transcript_id "g4.t1"; gene_id "g4";
# end gene g4
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_3.prfl --predictionStart=62338 --predictionEnd=73243 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_3.prfl --predictionStart=62338 --predictionEnd=73243 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[0..26]--> unknown_A (25) <--[4..13]--> unknown_B (16) <--[40..496]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10546, name = sample) -----
......@@ -19,12 +19,12 @@ sample AUGUSTUS gene 66254 68675 0.1 + . g1
sample AUGUSTUS transcript 66254 68675 0.1 + . g1.t1
sample AUGUSTUS exon 66254 66359 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 66312 66314 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.76 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.62 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.76 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.75 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.96 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.77 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.96 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 67338 67542 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.7 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.86 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
......@@ -64,6 +64,8 @@ sample AUGUSTUS protein_match 69572 69619 7.89 + 0 target "unknown_B[1..16]"; ta
# RRKGEEAVEISTSGFSARKLKKAKEQHASDGKTTYDNFLQTSLLTQGGNEVETSERIKVEEIEVAKVAVLTDEELFKACGGRTAHKGARHGLKLSGKI
# ARLEQQEREMLEKLQSKLKTTPETTLVPKSGKLIEETQHKVADSVDCSVEQATKPKKKKKSRTEESVEEIAPAQLEEPIKSKKKKKDKAEKAAKEYST
# HQAQDDPVQIKRRKNKTGKLEEEVQDVTEVEEAVKIKKKDKRQQGVEATEALSIETDEHVKSKKKRKTEDSSEETETPTKTKKKRKNKELV]
# sequence of block unknown_A 16 [DGLGKNNTGIAAPLKASLKFDNAGL] 41
# sequence of block unknown_B 49 [NDHWWERCFNEAASNV] 65
# end gene g2
###
# start gene g3
......@@ -145,4 +147,4 @@ sample AUGUSTUS tts 74808 74808 . + . transcript_id "g4.t1"; gene_id "g4";
# end gene g4
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_4.prfl --predictionStart=64425 --predictionEnd=74970 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_4.prfl --predictionStart=64425 --predictionEnd=74970 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[0..48]--> unknown_A (7) <--[9..17]--> unknown_B (13) <--[0..5]--> unknown_C (23) <--[11..39]--> unknown_E (104) <--[0..1]--> unknown_F (11) <--[17..768]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10570, name = sample) -----
......@@ -19,12 +19,12 @@ sample AUGUSTUS gene 66254 68675 0.51 + . g1
sample AUGUSTUS transcript 66254 68675 0.51 + . g1.t1
sample AUGUSTUS exon 66254 66359 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS start_codon 66312 66314 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.54 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.55 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.54 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.57 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 66360 67337 0.95 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS intron 67543 68133 0.76 + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 66312 66359 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 67338 67542 0.95 + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 67338 67542 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.57 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS CDS 68134 68297 0.86 + 2 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS exon 68134 68675 . + . transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS stop_codon 68295 68297 . + 0 transcript_id "g1.t1"; gene_id "g1";
sample AUGUSTUS tts 68675 68675 . + . transcript_id "g1.t1"; gene_id "g1";
......@@ -100,6 +100,11 @@ sample AUGUSTUS protein_match 71718 71720 10.3 - 0 target "unknown_A[1..1]"; tar
# LAPELAVQLEKHEQKRANLFKGNAKLPYIRPEEDPVLNDFKREMLFHRQAQSAVLEAIPRLHELGIKTRRPDDYFAEMAKSDEHMQKVRANLMAKQQG
# QAKSERIKQIREQRKMGKMLAKQTKVQREAEKKDMLDKLKKFRKGKLKNLDFLEDAKALESKQKQSAENRKKRNKKFGFGGKKKGLKRNTKSSSAGLD
# GDKSTRRQRGVKAGASVNKRLGKSRRIKAKGRK]
# sequence of block unknown_F 222 [LKNLDFLEDAK] 233
# sequence of block unknown_E 117 [FKREMLFHRQAQSAVLEAIPRLHELGIKTRRPDDYFAEMAKSDEHMQKVRANLMAKQQGQAKSERIKQIREQRKMGKMLAKQTKVQREAEKKDMLDKLKKFRKG] 221
# sequence of block unknown_C 60 [KMQLPWLERLDMINTLAPLAPEL] 83
# sequence of block unknown_B 42 [QRDKVNDVTKLLA] 55
# sequence of block unknown_A 21 [ELQAAFE] 28
# end gene g3
###
# start gene g4
......@@ -163,4 +168,4 @@ sample AUGUSTUS exon 76557 76647 . + . transcript_id "g4.t1"; gene_id "g4";
# end gene g4
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_5.prfl --predictionStart=66078 --predictionEnd=76647 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_5.prfl --predictionStart=66078 --predictionEnd=76647 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[108..1387]--> unknown_A (47) <--[0..7]--> unknown_B (9) <--[5..15]--> unknown_C (95) <--[0..1]--> unknown_D (29) <--[0..3]--> unknown_E (6) <--[7..192]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 14629, name = sample) -----
......@@ -191,6 +191,11 @@ sample AUGUSTUS protein_match 84061 84201 10.8 - 0 target "unknown_A[1..47]"; ta
# TRWMESNALVMLLPHGYDGGASEHSSCRIERFLQLSDSKETSADGDSVNVHVVNPTTPAQYYHVLRRQLARNFRKPLVVVAPKTLLRLPVATSTHEDF
# QPGTLFQNVLGDTTAKPEQVRKVILCSGKHYYALAEEREKRQAYDTAILRLESLSPFPVQELQAQLAQYGNVQSFVWSQEEHRNMGAWTFVRPRFENL
# IGQKLHYSGRCEAPTNATGIGNVHKREVDEILAGPFEL]
# sequence of block unknown_E 833 [ARNFRK] 839
# sequence of block unknown_D 804 [TSADGDSVNVHVVNPTTPAQYYHVLRRQL] 833
# sequence of block unknown_C 709 [KLEVAHSTLSEEAVLGFEYGMAIDNPNNLIIWEAQFGDFANGAQIIIDTFIVTGETRWMESNALVMLLPHGYDGGASEHSSCRIERFLQLSDSKE] 804
# sequence of block unknown_B 694 [EMYIPLNNM] 703
# sequence of block unknown_A 647 [KIDWSTAEAMAIGSLMYQGHNVRISGEDVGRGTFSHRHAMLVDQQTN] 694
# end gene g2
###
# start gene g3
......@@ -216,4 +221,4 @@ sample AUGUSTUS tts 91693 91693 . + . transcript_id "g3.t1"; gene_id "g3";
# end gene g3
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_6.prfl --predictionStart=77357 --predictionEnd=91985 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_6.prfl --predictionStart=77357 --predictionEnd=91985 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[0..436]--> unknown_A (160) <--[0..3]--> unknown_B (26) <--[2..24]--> unknown_C (14) <--[4..160]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10717, name = sample) -----
......@@ -56,7 +56,10 @@ sample AUGUSTUS protein_match 169093 169134 2 + 0 target "unknown_C[1..14]"; tar
# protein sequence = [MARLYDSRTTIFSPEGRLYQVEYAMEAASQSNTCLGILAKNGVILATERSVDKLLDSSIPAPRICRLNEDAACCATGN
# KADGNVLTTELRLIAQQYVSTYGEMIPCEQLVTNLCDIKQAYTQYGGKRPFGVSFLYMGWDCRFGFQLYQSDPSGNYSGWKATCIGRKSGAAMEMLQK
# ELFSKGYASPSLEEAKDVAIKVMGMTLDRDSLTPAKLEMAVLQRFYNTTIFHILEKIEVHNLIQKHNILQFQIARRKY]
# sequence of block unknown_A 23 [AMEAASQSNTCLGILAKNGVILATERSVDKLLDSSIPAPRICRLNEDAACCATGNKADGNVLTTELRLIAQQYVSTYGEMIPCEQLVTNLCDIKQAYTQYGGKRPFGVSFLYMGWDCRFGFQLYQSDPSGNYSGWKATCIGRKSGAAMEMLQKELFSKGY] 183
# sequence of block unknown_B 186 [SLEEAKDVAIKVMGMTLDRDSLTPAK] 212
# sequence of block unknown_C 233 [EVHNLIQKHNILQF] 247
# end gene g2
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_7.prfl --predictionStart=163394 --predictionEnd=174110 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
......@@ -2,11 +2,11 @@
# Using native and syntenically mapped cDNA alignments to improve de novo gene finding
# Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
# No extrinsic information on sequences given.
# Initialising the parameters ...
# Initialising the parameters using config directory /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/config/ ...
# Using protein profile unknown
# --[51..127]--> unknown_A (43) <--[2..166]--
# fly version. Use default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1214242381_.temp is in fasta format.
# fly version. Using default transition matrix.
# Looks like ./tmp/sampleSAMPLE_1279401836_.temp is in fasta format.
# We have hints for 0 sequences and for 0 of the sequences in the input set.
#
# ----- prediction on sequence number 1 (length = 10871, name = sample) -----
......@@ -67,6 +67,7 @@ sample AUGUSTUS protein_match 233631 233759 4.4 + 0 target "unknown_A[1..43]"; t
# protein sequence = [MGARQSQSREARSVSMENPTPAGVIDISDDVVKRLKAGISQQAREHAAAAEDSKPAPKPTAKAAAKPAASSPAAPAPK
# VSSYPAAVPIYVQGGGHTISAADVQRQMNQELIKNDELWKERMAKLEENLKKTNTILEKEYANAVDNVHKRFVSTASSHKVPPCQDLKSQLLACYRAH
# PGETLKCMEEVAQFRQCIDLHRVQKLDAEPETLKVAKAA]
# sequence of block unknown_A 104 [QMNQELIKNDELWKERMAKLEENLKKTNTILEKEYANAVDNVH] 147
# end gene g2
###
# start gene g3
......@@ -117,4 +118,4 @@ sample AUGUSTUS tss 238509 238509 . - . transcript_id "g3.t1"; gene_id "g3";
# end gene g3
###
# command line:
# augustus --codingseq=1 --proteinprofile=sample_data/example/prfl/BUSCO_8.prfl --predictionStart=228045 --predictionEnd=238915 --species=fly ./tmp/sampleSAMPLE_1214242381_.temp
# /home/osboxes/BUSCOVM/augustus/augustus-3.2.2/bin/augustus --codingseq=1 --proteinprofile=./sample_data/example/prfl/BUSCO_8.prfl --predictionStart=228045 --predictionEnd=238915 --species=fly ./tmp/sampleSAMPLE_1279401836_.temp
#exon model parameters
# begin of content independent part
# start codon probabilities
[STARTCODONS]
# number of start codons:
1
# start codons and their probabilities
ATG 1
# Length distributions
[LENGTH]
......
#
# BUSCO_SAMPLE_1214242381 parameters.
# BUSCO_SAMPLE_1279401836 parameters.
#
# date : 19.12.2006
#
......@@ -68,21 +68,21 @@ UTR off # predict untranslated regions
# type of weighing, one of 1 = equalWeights, 2 = gcContentClasses, 3 = multiNormalKernel
/BaseCount/weighingType 3
# file with the weight matrix (only for multiNormalKernel type weighing)
/BaseCount/weightMatrixFile BUSCO_SAMPLE_1214242381_weightmatrix.txt # change this to your species if at all neccessary
/BaseCount/weightMatrixFile BUSCO_SAMPLE_1279401836_weightmatrix.txt # change this to your species if at all neccessary
# Properties for IGenicModel
# ----------------------------
/IGenicModel/verbosity 0
/IGenicModel/infile BUSCO_SAMPLE_1214242381_igenic_probs.pbl # change this and the other five filenames *_probs.pbl below to your species
/IGenicModel/outfile BUSCO_SAMPLE_1214242381_igenic_probs.pbl
/IGenicModel/infile BUSCO_SAMPLE_1279401836_igenic_probs.pbl # change this and the other five filenames *_probs.pbl below to your species
/IGenicModel/outfile BUSCO_SAMPLE_1279401836_igenic_probs.pbl
/IGenicModel/patpseudocount 5.0
/IGenicModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k
# Properties for ExonModel
# ----------------------------
/ExonModel/verbosity 3
/ExonModel/infile BUSCO_SAMPLE_1214242381_exon_probs.pbl
/ExonModel/outfile BUSCO_SAMPLE_1214242381_exon_probs.pbl
/ExonModel/infile BUSCO_SAMPLE_1279401836_exon_probs.pbl
/ExonModel/outfile BUSCO_SAMPLE_1279401836_exon_probs.pbl
/ExonModel/patpseudocount 5.0
/ExonModel/minPatSum 233.3
/ExonModel/k 4 # order of the Markov chain for content model
......@@ -98,8 +98,8 @@ UTR off # predict untranslated regions
# Properties for IntronModel
# ----------------------------
/IntronModel/verbosity 0
/IntronModel/infile BUSCO_SAMPLE_1214242381_intron_probs.pbl
/IntronModel/outfile BUSCO_SAMPLE_1214242381_intron_probs.pbl
/IntronModel/infile BUSCO_SAMPLE_1279401836_intron_probs.pbl
/IntronModel/outfile BUSCO_SAMPLE_1279401836_intron_probs.pbl
/IntronModel/patpseudocount 5.0
/IntronModel/k 4 # order of the Markov chain for content model, keep equal to /ExonModel/k
/IntronModel/slope_of_bandwidth 0.4
......@@ -107,7 +107,7 @@ UTR off # predict untranslated regions
/IntronModel/asspseudocount 0.00266
/IntronModel/dsspseudocount 0.0005
/IntronModel/dssneighborfactor 0.00173
#/IntronModel/splicefile BUSCO_SAMPLE_1214242381_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one
#/IntronModel/splicefile BUSCO_SAMPLE_1279401836_splicefile.txt # this optional file contains additional windows around splice sites for training, uncomment if you have one
/IntronModel/sf_with_motif false # if true the splice file is also used to train the branch point region
/IntronModel/d 100 # constraint: this must be larger than 4 + /Constant/dss_end + /Constant/ass_upwindow_size + /Constant/ass_start
/IntronModel/ass_motif_memory 3
......@@ -116,8 +116,8 @@ UTR off # predict untranslated regions
# Properties for UtrModel
# ----------------------------
/UtrModel/verbosity 3
/UtrModel/infile BUSCO_SAMPLE_1214242381_utr_probs.pbl
/UtrModel/outfile BUSCO_SAMPLE_1214242381_utr_probs.pbl
/UtrModel/infile BUSCO_SAMPLE_1279401836_utr_probs.pbl
/UtrModel/outfile BUSCO_SAMPLE_1279401836_utr_probs.pbl
/UtrModel/k 4
/UtrModel/utr5patternweight 0.5
/UtrModel/utr3patternweight 0.5
......
BUSCO_5 sample 66078 76647
BUSCO_6 sample 77357 91985
BUSCO_7 sample 163394 174110
BUSCO_1 sample 25227 35708
BUSCO_4 sample 64425 74970
BUSCO_2 sample 27021 51425
BUSCO_3 sample 62338 73243
BUSCO_1 sample 25227 35708
BUSCO_5 sample 66078 76647
BUSCO_8 sample 228045 238915
BUSCO_7 sample 163394 174110
BUSCO_6 sample 77357 91985
BUSCO_3 sample 62338 73243
# TBLASTN 2.4.0+
# TBLASTN 2.2.31+
# Query: BUSCO_3
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 2 hits found
BUSCO_3 sample 59.322 59 21 1 16 74 67338 67505 6.72e-14 67.8
BUSCO_3 sample 80.556 36 7 0 95 130 68136 68243 1.16e-12 63.9
# TBLASTN 2.4.0+
BUSCO_3 sample 59.32 59 21 1 16 74 67338 67505 7e-14 67.8
BUSCO_3 sample 80.56 36 7 0 95 130 68136 68243 1e-12 63.9
# TBLASTN 2.2.31+
# Query: BUSCO_4
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
BUSCO_4 sample 73.077 182 49 0 1 182 69425 69970 1.48e-64 219
# TBLASTN 2.4.0+
BUSCO_4 sample 73.08 182 49 0 1 182 69425 69970 3e-63 219
# TBLASTN 2.2.31+
# Query: BUSCO_6
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 11 hits found
BUSCO_6 sample 66.409 259 85 2 286 543 85106 84333 0.0 321
BUSCO_6 sample 80.142 141 28 0 544 684 84267 83845 0.0 248
BUSCO_6 sample 76.991 113 26 0 680 792 83803 83465 0.0 192
BUSCO_6 sample 72.414 29 8 0 262 290 85254 85168 0.0 44.3
BUSCO_6 sample 75.410 61 15 0 789 849 83058 82876 6.53e-18 83.6
BUSCO_6 sample 50.000 62 23 2 836 897 82697 82536 5.23e-12 63.9
BUSCO_6 sample 69.048 42 13 0 172 213 86380 86255 2.97e-11 61.6
BUSCO_6 sample 70.370 54 16 0 211 264 85767 85606 3.13e-11 61.6
BUSCO_6 sample 74.286 35 9 0 882 916 82461 82357 7.01e-09 53.9
BUSCO_6 sample 79.167 24 5 0 54 77 86985 86914 4.77e-06 44.7
BUSCO_6 sample 71.111 45 12 1 88 131 86706 86572 4.78e-04 37.7
# TBLASTN 2.4.0+
BUSCO_6 sample 66.41 259 85 2 286 543 85106 84333 0.0 321
BUSCO_6 sample 80.14 141 28 0 544 684 84267 83845 0.0 248
BUSCO_6 sample 76.99 113 26 0 680 792 83803 83465 0.0 192
BUSCO_6 sample 72.41 29 8 0 262 290 85254 85168 0.0 44.3
BUSCO_6 sample 75.41 61 15 0 789 849 83058 82876 7e-18 83.6
BUSCO_6 sample 50.00 62 23 2 836 897 82697 82536 5e-12 63.9
BUSCO_6 sample 69.05 42 13 0 172 213 86380 86255 3e-11 61.6
BUSCO_6 sample 70.37 54 16 0 211 264 85767 85606 3e-11 61.6
BUSCO_6 sample 74.29 35 9 0 882 916 82461 82357 7e-09 53.9
BUSCO_6 sample 79.17 24 5 0 54 77 86985 86914 5e-06 44.7
BUSCO_6 sample 71.11 45 12 1 88 131 86706 86572 5e-04 37.7
# TBLASTN 2.2.31+
# Query: BUSCO_2
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 7 hits found
BUSCO_2 sample 85.000 80 12 0 365 444 46186 46425 5.32e-39 145
BUSCO_2 sample 81.081 74 14 0 298 371 45523 45744 2.40e-32 125
BUSCO_2 sample 93.750 48 3 0 262 309 45267 45410 4.11e-23 97.1
BUSCO_2 sample 90.000 50 5 0 186 235 42013 42162 5.02e-23 97.1
BUSCO_2 sample 89.130 46 5 0 140 185 41480 41617 5.23e-21 90.5
BUSCO_2 sample 90.625 32 3 0 232 263 42697 42792 1.22e-11 61.2
BUSCO_2 sample 56.098 82 28 1 1 82 32021 32242 1.84e-11 60.5
# TBLASTN 2.4.0+
BUSCO_2 sample 85.00 80 12 0 365 444 46186 46425 3e-38 145
BUSCO_2 sample 81.08 74 14 0 298 371 45523 45744 5e-32 125
BUSCO_2 sample 93.75 48 3 0 262 309 45267 45410 4e-23 97.1
BUSCO_2 sample 90.00 50 5 0 186 235 42013 42162 5e-23 97.1
BUSCO_2 sample 89.13 46 5 0 140 185 41480 41617 5e-21 90.5
BUSCO_2 sample 90.62 32 3 0 232 263 42697 42792 1e-11 61.2
BUSCO_2 sample 56.10 82 28 1 1 82 32021 32242 2e-11 60.5
# TBLASTN 2.2.31+
# Query: BUSCO_5
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
BUSCO_5 sample 61.053 190 55 1 23 193 71647 71078 3.11e-58 196
# TBLASTN 2.4.0+
BUSCO_5 sample 61.05 190 55 1 23 193 71647 71078 7e-57 196
# TBLASTN 2.2.31+
# Query: BUSCO_1
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 2 hits found
BUSCO_1 sample 70.330 91 27 0 104 194 30499 30227 2.67e-54 123
BUSCO_1 sample 78.947 57 12 0 53 109 30708 30538 2.67e-54 100
# TBLASTN 2.4.0+
BUSCO_1 sample 70.33 91 27 0 104 194 30499 30227 3e-54 123
BUSCO_1 sample 78.95 57 12 0 53 109 30708 30538 3e-54 100
# TBLASTN 2.2.31+
# Query: BUSCO_7
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 1 hits found
BUSCO_7 sample 62.083 240 87 2 212 448 168394 169110 2.94e-95 310
# TBLASTN 2.4.0+
BUSCO_7 sample 62.08 240 87 2 212 448 168394 169110 1e-93 310
# TBLASTN 2.2.31+
# Query: BUSCO_8
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# Fields: query id, subject id, % identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score
# 2 hits found
BUSCO_8 sample 58.654 104 43 0 80 183 233604 233915 2.50e-28 105
BUSCO_8 sample 61.111 36 10 1 1 32 233045 233152 3.31e-06 41.2
# TBLASTN 2.4.0+
BUSCO_8 sample 58.65 104 43 0 80 183 233604 233915 2e-27 105
BUSCO_8 sample 61.11 36 10 1 1 32 233045 233152 4e-06 41.2
# TBLASTN 2.2.31+
# Query: BUSCO_9
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# 0 hits found
# TBLASTN 2.4.0+
# TBLASTN 2.2.31+
# Query: BUSCO_10
# Database: ./tmp/SAMPLE_1214242381
# Database: ./tmp/SAMPLE_1279401836
# 0 hits found
# BLAST processed 10 queries