maker_opts_swissprotmammals_plus_others_plus_ncrna.ctl

#-----Genome (these are always required)
genome=
model_org=vertebrates
protein=$HOME/maker_control_files/swissprot_mammals.cdhit.fasta,$HOME/maker_control_files/Homo_sapiens.GRCh38.pep.all.fa,$HOME/maker_control_files/GCF_000001635.26_GRCm38.p6_protein.faa,$HOME/maker_control_files/Ursus_americanus.ASM334442v1.pep.all.fa
repeat_protein=/mnt/lustre/software/anaconda/colsa/envs/maker-3.01.02/local/src/maker/data/te_proteins.fasta
est=/mnt/lustre/macmaneslab/macmanes/maker_control_files/refseq/splits/ncRNA_other_sp.fasta

organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
est_pass=1 #use ESTs in maker_gff: 1 = yes, 0 = no
altest_pass=1 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=1 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=1 #use repeats in maker_gff: 1 = yes, 0 = no
model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no
pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no
other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)
altest=

#-----Protein Homology Evidence (for best results provide a file for at least one)

#-----Repeat Masking (leave values blank to skip repeat masking)
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

#-----Gene Prediction
run_evm=0 #run EvidenceModeler, 1 = yes, 0 = no
est2genome=1 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=1 #infer predictions from protein homology, 1 = yes, 0 = no
trna=0 #find tRNAs with tRNAscan, 1 = yes, 0 = no


#-----External Application Behavior Options
alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases
cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=5000 #skip genome contigs below this length (under 10kb are often useless)

pred_flank=2000 #flank for extending evidence clusters sent to gene predictors
pred_stats=1 #report AED and QI statistics for all predictions as well as models
AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)
min_protein=0 #require at least this many amino acids in predicted proteins
alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no
map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)

split_hit=30000 #length for the splitting of hits (expected max intron size for evidence alignments)
min_intron=20 #minimum intron length (used for alignment polishing)
single_exon=1 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'
correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=4 #number of times to try a contig if there is a failure for some reason
clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no
clean_up=1 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no
TMP= #specify a directory other than the system default temporary directory for temporary files