# Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
# 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 using config directory /gscratch/scrubbed/samwhite/outputs/20200924_cbai_genome_v1.01_busco/cbai_genome_v1.01.fasta_augustus/config/ ...
# Using protein profile unknown
# --[0..81]--> unknown_A (14) <--[0..3]--> unknown_B (24) <--[2..5]--> unknown_C (31) <--[17..101]--> unknown_E (33) <--[1..25]--> unknown_F (19) <--[0..1]--> unknown_G (7) <--[0..1]--> unknown_H (13) <--[2..11]--> unknown_I (13) <--[6..9]--> unknown_J (53) <--[0..1]--> unknown_K (50) <--[0..1]--> unknown_L (9) <--[1..4]--> unknown_M (20) <--[7..24]--> unknown_O (17) <--[1..12]--> unknown_P (23) <--[9..25]--> unknown_R (18) <--[0..13]--> unknown_S (13) <--[0..1]--> unknown_T (21) <--[0..1]--> unknown_U (13) <--[10..16]--> unknown_W (18) <--[2..35]--> unknown_X (17) <--[1..5]--> unknown_Y (14) <--[11..25]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_3281cbai_genome_v1.01.fasta_145855183_.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 = 4229, name = contig_3281) -----
#
# Predicted genes for sequence number 1 on both strands
# (none)
# command line:
# /gscratch/srlab/programs/Augustus-3.3.2/bin/augustus --codingseq=1 --proteinprofile=/gscratch/srlab/sam/data/databases/BUSCO/metazoa_odb9/prfl/EOG091G09YB.prfl --predictionStart=0  --predictionEnd=8910  --species=fly --progress=true ./tmp/contig_3281cbai_genome_v1.01.fasta_145855183_.temp