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main_sbatch7.sh
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## version 2 for test genomes
# genome ORGID ORGNASIM
# t1 iLJ478 NC_000853.1 243274 Thermotoga maritima MSB8 neg
# t2 iJN1463 NC_002947.4 160488 Pseudomonas putida KT2440 neg
# t2 iCN900 AM180355.1 272563 Clostridioides difficile 630 pos
# t4 iAF1260 NC_000913.3 83333 Escherichia coli str. K-12 substr. MG1655 neg
# t4 iAF987 CP000148.1 269799 Geobacter metallireducens GS-15 neg
# t5 iNJ661 NC_000962.3 83332 Mycobacterium tuberculosis H37Rv pos
# t4 iYO844 AL009126.3 224308 Bacillus subtilis subsp. subtilis str. 168 pos
# all ec reward =0.1
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 0 iLJ478_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 0 0 iJN1463_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 0 iCN900_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 0 0 iAF1260_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 0 0 iAF987_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 0 0 iNJ661_allec default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 0 0 iYO844_allec default
# ## block only
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 0 iLJ478_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 1 0 iJN1463_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 0 iCN900_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 1 0 iAF1260_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 1 0 iAF987_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 0 iNJ661_block_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 1 0 iYO844_block_$rname default
# ## flux only
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 1 iLJ478_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 0 1 iJN1463_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 1 iCN900_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 0 1 iAF1260_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 0 1 iAF987_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 0 1 iNJ661_flux_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 0 1 iYO844_flux_$rname default
# ## block and flux
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 1 iLJ478_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 1 1 iJN1463_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 1 iCN900_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 1 1 iAF1260_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 1 1 iAF987_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 1 iNJ661_fluxblock_$rname default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 1 1 iYO844_fluxblock_$rname default
## test reward scale from 0.1 to 1.0
# Test reward scale from 0.1 to 1.0
echo "Starting reward tests"
# rewards=(0.1 0.3 0.5 0.7 1.0)
# rewards=(0.9)
# rewards=(0.05 1.5 2.0 3.0 )
# rewards=(0.05 0.2 5.0)
typrds=(allec block flux fluxblock)
# Iterate over reward scales
for reward in "${rewards[@]}"; do
if (( $(echo "$reward < 1.0" | bc -l) )); then
rname="p$(echo "$reward" | sed 's/\.//g')"
else
rname=$(printf "%.0f" "$reward")
fi
# Iterate over types
for typrd in "${typrds[@]}"; do
if [[ "$typrd" == "allec" ]]; then
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 0 iLJ478_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 0 0 iJN1463_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 0 iCN900_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 0 0 iAF1260_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 0 0 iAF987_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 0 0 iNJ661_allec_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 0 0 iYO844_allec_"$rname" default "$reward"
elif [[ "$typrd" == "block" ]]; then
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 0 iLJ478_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 1 0 iJN1463_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 0 iCN900_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 1 0 iAF1260_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 1 0 iAF987_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 0 iNJ661_block_"$rname" default "$reward"
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 1 0 iYO844_block_"$rname" default "$reward"
elif [[ "$typrd" == "flux" ]]; then
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 1 iLJ478_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 0 1 iJN1463_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 1 iCN900_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 0 1 iAF1260_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 0 1 iAF987_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 0 1 iNJ661_flux_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 0 1 iYO844_flux_$rname default $reward
elif [[ "$typrd" == "fluxblock" ]]; then
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 1 iLJ478_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 1 1 iJN1463_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 1 iCN900_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 1 1 iAF1260_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/CP000148.1_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/CP000148.1_t4_maxsep_df.pkl negative 1 1 iAF987_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 1 iNJ661_fluxblock_$rname default $reward
sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 1 1 iYO844_fluxblock_$rname default $reward
fi
done
done
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 1 --name iLJ478_flux_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 1 --name iJN1463_flux_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram negative --block_flage 1 --flux_flage 1 --name iLJ478_fluxblock_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram negative --block_flage 1 --flux_flage 1 --name iAF1260_fluxblock_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram positive --block_flage 1 --flux_flage 1 --name iNJ661_fluxblock_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl --file_type 7 --reward 0.5 --iter 10 --cpu 8 --gram positive --block_flage 1 --flux_flage 1 --name iYO844_fluxblock_p05 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl --file_type 7 --reward 0.7 --iter 10 --cpu 8 --gram positive --block_flage 0 --flux_flage 0 --name iCN900_allec_p07 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl --file_type 7 --reward 0.7 --iter 10 --cpu 8 --gram negative --block_flage 1 --flux_flage 0 --name iLJ478_block_p07 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl --file_type 7 --reward 0.7 --iter 10 --cpu 8 --gram positive --block_flage 1 --flux_flage 0 --name iCN900_block_p07 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl --file_type 7 --reward 0.7 --iter 10 --cpu 8 --gram negative --block_flage 1 --flux_flage 1 --name iJN1463_fluxblock_p07 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl --file_type 7 --reward 0.7 --iter 10 --cpu 8 --gram positive --block_flage 1 --flux_flage 1 --name iCN900_fluxblock_p07 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl --file_type 7 --reward 1.0 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 0 --name iLJ478_allec_1 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl --file_type 7 --reward 1.0 --iter 10 --cpu 8 --gram positive --block_flage 0 --flux_flage 0 --name iCN900_allec_1 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl --file_type 7 --reward 1.0 --iter 10 --cpu 8 --gram positive --block_flage 1 --flux_flage 0 --name iNJ661_block_1 --threshold 8 --media default
# python mainclean_interation_v2.py --input_file /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta --cleanfile /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl --file_type 7 --reward 1.0 --iter 10 --cpu 8 --gram negative --block_flage 0 --flux_flage 1 --name iLJ478_flux_1 --threshold 8 --media default
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 0 iLJ478_flux_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 0 0 iJN1463_flux_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 0 iLJ478_fluxblock_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000913.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000913.3_t4_maxsep_df.pkl negative 1 0 iAF1260_fluxblock_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 0 iNJ661_fluxblock_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AL009126.3_t4.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AL009126.3_t4_maxsep_df.pkl positive 1 0 iYO844_fluxblock_p05 default 0.5
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 0 iCN900_allec_p07 default 0.7
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 1 0 iLJ478_block_p07 default 0.7
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 0 iCN900_block_p07 default 0.7
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_002947.4_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_002947.4_t2_maxsep_df.pkl negative 1 1 iJN1463_fluxblock_p07 default 0.7
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 1 1 iCN900_fluxblock_p07 default 0.7
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 0 iLJ478_allec_1 default 1.0
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/AM180355.1_t2.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/AM180355.1_t2_maxsep_df.pkl positive 0 0 iCN900_allec_1 default 1.0
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000962.3_t5.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000962.3_t5_maxsep_df.pkl positive 1 0 iNJ661_block_1 default 1.0
# sbatch maincleaniterv2.sh /ibex/user/niuk0a/CLEAN/app/data/inputs/NC_000853.1_t1.fasta /ibex/user/niuk0a/CLEAN/app/results/inputs/NC_000853.1_t1_maxsep_df.pkl negative 0 1 iLJ478_flux_1 default 1.0