module load funannotate/1.5.0
module load signalp
module load python/2.7.14
module load eggnog

funannotate clean -i Sceloporus_PBJ.fasta --minlen 7000000 -o Scel_cleaned.fasta
funannotate sort -i Scel_cleaned.fasta -b scaffold -o Scel_sorted.fasta
funannotate mask -i Scel_sorted.fasta --cpus 10 -o Scel_masked.fasta

funannotate train -i Scel_masked.fasta -o Sceloporus --left left.fastq --right right.fastq --max_intronlen 500000 --species "Sceloporus undulatus" --cpus 20

funannotate predict \
-i Scel_masked.fasta \
-s "Sceloporus undulatus" \
-o Sceloporus \
--busco_seed_species human \
--busco_db tetrapoda \
--organism other \
--repeats2evm \
--cpus 20 \
--max_intronlen 20000 \
--optimize_augustus

funannotate update -i Sceloporus --species "Sceloporus undulatus" --trinity Sceloporus/predict_results/Sceloporus_undulatus.transcripts.fa --left_norm left_normalized.fastq --right_norm right_normalized.fastq --cpus 20

funannotate iprscan -i Sceloporus -m local -c 10 --iprscan_path /tools/interproscan-5.17-56.0 -o iprscan.xml

funannotate remote -i Sceloporus -m phobius -e dsw0002@auburn.edu

python /tools/eggnog-1/emapper.py -i Sceloporus/predict_results/Sceloporus_undulatus.proteins.fa --output Scel_eggnog -m diamond --cpu 10

funannotate annotate -i Sceloporus --eggnog Scel_eggnog.emapper.annotations --iprscan iprscan.xml --busco_db tetrapoda --cpus 10 --force

