# 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..112]--> unknown_A (49) <--[0..1]--> unknown_B (102) <--[0..1]--> unknown_C (9) <--[2..6]--> unknown_D (24) <--[2..13]--> unknown_E (27) <--[1..2]--> unknown_F (23) <--[0..1]--> unknown_G (7) <--[0..1]--> unknown_H (20) <--[0..1]--> unknown_I (36) <--[2..9]--> unknown_J (22) <--[0..86]--> unknown_K (36) <--[14..38]--> unknown_M (22) <--[0..100]--
# fly version. Using default transition matrix.
# Looks like ./tmp/contig_2929cbai_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 = 10336, name = contig_2929) -----
#
# 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/EOG091G060D.prfl --predictionStart=19511  --predictionEnd=29846  --species=fly --progress=true ./tmp/contig_2929cbai_genome_v1.01.fasta_145855183_.temp