# 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..83]--> unknown_A (9) <--[2..7]--> unknown_B (34) <--[0..1]--> unknown_C (22) <--[0..2]--> unknown_D (13) <--[2..6]--> unknown_E (33) <--[0..8]--> unknown_F (27) <--[3..58]--> unknown_G (49) <--[1..39]--> unknown_H (33) <--[0..1]--> unknown_I (16) <--[0..47]--> unknown_J (19) <--[2..7]--> unknown_K (47) <--[2..15]--> unknown_L (59) <--[7..90]--> unknown_N (30) <--[11..33]--> unknown_P (16) <--[2..15]--> unknown_Q (50) <--[2..14]--> unknown_R (17) <--[4..11]--> unknown_S (51) <--[0..35]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_2744cbai_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 = 10156, name = contig_2744) -----
#
# 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/EOG091G0703.prfl --predictionStart=37678  --predictionEnd=47833  --species=fly --progress=true ./tmp/contig_2744cbai_genome_v1.01.fasta_145855183_.temp