Index

Symbols

--additional_genes run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --additional_logic run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --additional_min_categories run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --aws_s3 run_dbcan-database command line option --base_pair_distance run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --batch_size run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --batch_size_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --bitscore_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --CAZyme_pair_num run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --cgc run_dbcan-database command line option --coverage_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --coverage_threshold_dbcan run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --coverage_threshold_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --coverage_threshold_peptidase run_dbcan-gff_process command line option --coverage_threshold_pfam run_dbcan-Pfam_null_cgc command line option --coverage_threshold_stp run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --coverage_threshold_sulfatase run_dbcan-gff_process command line option --coverage_threshold_tc run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --coverage_threshold_tf run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --coverage_threshold_tf_diamond run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --csv_buffer_size run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --csv_buffer_size_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --db_dir run_dbcan-CAZyme_annotation command line option run_dbcan-database command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option --deeptmhmm_dir run_dbcan-CAZyme_annotation command line option --deeptmhmm_python run_dbcan-CAZyme_annotation command line option --e_value_threshold run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --e_value_threshold_dbcan run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --e_value_threshold_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --e_value_threshold_peptidase run_dbcan-gff_process command line option --e_value_threshold_pfam run_dbcan-Pfam_null_cgc command line option --e_value_threshold_stp run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --e_value_threshold_sulfatase run_dbcan-gff_process command line option --e_value_threshold_tc run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --e_value_threshold_tf run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --e_value_threshold_tf_diamond run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --enable_memory_monitoring run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --enable_memory_monitoring_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --env run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --evalue_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --extend_bp run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --extend_gene_count run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --extend_mode run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --extra_pair_type run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --extra_pair_type_num run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --feature_type run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --force_topology run_dbcan-CAZyme_annotation command line option --fungi run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --gff_type run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --hmmcov run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --hmmevalue run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --identity_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --input_gff run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --input_raw_data run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --large run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --large_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --large_input_threshold_mb run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --large_input_threshold_mb_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --log-file run_dbcan command line option run_dbcan-CAZyme_annotation command line option run_dbcan-cgc_circle_plot command line option run_dbcan-cgc_finder command line option run_dbcan-database command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option --log-level run_dbcan command line option run_dbcan-CAZyme_annotation command line option run_dbcan-cgc_circle_plot command line option run_dbcan-cgc_finder command line option run_dbcan-database command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option --max_memory_usage run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --max_memory_usage_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --max_retries run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --max_retries_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --memory_safety_factor run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --memory_safety_factor_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option

--methods run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --min_cluster_genes run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --min_core_cazyme run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --mode run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --no-cgc run_dbcan-database command line option --no-enable_memory_monitoring run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --no-enable_memory_monitoring_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --no-force_topology run_dbcan-CAZyme_annotation command line option --no-fungi run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --no-large run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --no-large_dbsub run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --no-overwrite run_dbcan-database command line option --no-prokaryotic run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --no-resume run_dbcan-database command line option --no-run_deeptmhmm run_dbcan-CAZyme_annotation command line option --no-run_signalp run_dbcan-CAZyme_annotation command line option --no-use_null_genes run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --no-verify-ssl run_dbcan-database command line option --null_from_gff run_dbcan-Pfam_null_cgc command line option --num_null_gene run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --num_of_domains_substrate_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --num_of_protein_substrate_cutoff run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --odbcan_sub run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --odbcanpul run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --out run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --output_dir run_dbcan-CAZyme_annotation command line option run_dbcan-cgc_circle_plot command line option run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option --prodigal-gff-streaming run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --prodigal-streaming-threshold-mb run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --prokaryotic run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option --pul run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --rerun run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --resume run_dbcan-database command line option --retries run_dbcan-database command line option --run_deeptmhmm run_dbcan-CAZyme_annotation command line option --run_pfam run_dbcan-Pfam_null_cgc command line option --run_signalp run_dbcan-CAZyme_annotation command line option --signalp_org run_dbcan-CAZyme_annotation command line option --substrate_scors run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --threads run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option --timeout run_dbcan-database command line option --total_pair_num run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --uniq_pul_gene_hit_num run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --uniq_query_cgc_gene_num run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option --use_distance run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --use_null_genes run_dbcan-cgc_finder command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --verbose run_dbcan command line option run_dbcan-CAZyme_annotation command line option run_dbcan-cgc_circle_plot command line option run_dbcan-cgc_finder command line option run_dbcan-database command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option --verbose_option run_dbcan-CAZyme_annotation command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option --verify-ssl run_dbcan-database command line option --workdir run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -bsc run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -cov run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -cpn run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -env run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -ept run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -eptn run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -evalue run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -hmmcov run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -hmmevalue run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -iden run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -ndsc run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -npsc run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -o run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -odbcan_sub run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -odbcanpul run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -rerun run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -subs run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -tpn run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -upghn run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -uqcgn run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option -v run_dbcan command line option run_dbcan-CAZyme_annotation command line option run_dbcan-cgc_circle_plot command line option run_dbcan-cgc_finder command line option run_dbcan-database command line option run_dbcan-easy_CGC command line option run_dbcan-easy_substrate command line option run_dbcan-gff_process command line option run_dbcan-Pfam_null_cgc command line option run_dbcan-substrate_prediction command line option -w run_dbcan-easy_substrate command line option run_dbcan-substrate_prediction command line option

R

run_dbcan command line option --log-file --log-level --verbose -v run_dbcan-CAZyme_annotation command line option --batch_size --batch_size_dbsub --coverage_threshold_dbcan --coverage_threshold_dbsub --csv_buffer_size --csv_buffer_size_dbsub --db_dir --deeptmhmm_dir --deeptmhmm_python --e_value_threshold --e_value_threshold_dbcan --e_value_threshold_dbsub --enable_memory_monitoring --enable_memory_monitoring_dbsub --force_topology --input_raw_data --large --large_dbsub --large_input_threshold_mb --large_input_threshold_mb_dbsub --log-file --log-level --max_memory_usage --max_memory_usage_dbsub --max_retries --max_retries_dbsub --memory_safety_factor --memory_safety_factor_dbsub --methods --mode --no-enable_memory_monitoring --no-enable_memory_monitoring_dbsub --no-force_topology --no-large --no-large_dbsub --no-run_deeptmhmm --no-run_signalp --output_dir --run_deeptmhmm --run_signalp --signalp_org --threads --verbose --verbose_option -v run_dbcan-cgc_circle_plot command line option --log-file --log-level --output_dir --verbose -v run_dbcan-cgc_finder command line option --additional_genes --additional_logic --additional_min_categories --base_pair_distance --extend_bp --extend_gene_count --extend_mode --feature_type --log-file --log-level --min_cluster_genes --min_core_cazyme --no-use_null_genes --num_null_gene --output_dir --use_distance --use_null_genes --verbose -v run_dbcan-database command line option --aws_s3 --cgc --db_dir --log-file --log-level --no-cgc --no-overwrite --no-resume --no-verify-ssl --resume --retries --timeout --verbose --verify-ssl -v run_dbcan-easy_CGC command line option --additional_genes --additional_logic --additional_min_categories --base_pair_distance --batch_size --batch_size_dbsub --coverage_threshold_dbcan --coverage_threshold_dbsub --coverage_threshold_stp --coverage_threshold_tc --coverage_threshold_tf --coverage_threshold_tf_diamond --csv_buffer_size --csv_buffer_size_dbsub --db_dir --e_value_threshold --e_value_threshold_dbcan --e_value_threshold_dbsub --e_value_threshold_stp --e_value_threshold_tc --e_value_threshold_tf --e_value_threshold_tf_diamond --enable_memory_monitoring --enable_memory_monitoring_dbsub --extend_bp --extend_gene_count --extend_mode --feature_type --fungi --gff_type --input_gff --input_raw_data --large --large_dbsub --large_input_threshold_mb --large_input_threshold_mb_dbsub --log-file --log-level --max_memory_usage --max_memory_usage_dbsub --max_retries --max_retries_dbsub --memory_safety_factor --memory_safety_factor_dbsub --methods --min_cluster_genes --min_core_cazyme --mode --no-enable_memory_monitoring --no-enable_memory_monitoring_dbsub --no-fungi --no-large --no-large_dbsub --no-prokaryotic --no-use_null_genes --num_null_gene --output_dir --prodigal-gff-streaming --prodigal-streaming-threshold-mb --prokaryotic --threads --use_distance --use_null_genes --verbose --verbose_option -v run_dbcan-easy_substrate command line option --additional_genes --additional_logic --additional_min_categories --base_pair_distance --batch_size --batch_size_dbsub --bitscore_cutoff --CAZyme_pair_num --coverage_cutoff --coverage_threshold_dbcan --coverage_threshold_dbsub --coverage_threshold_stp --coverage_threshold_tc --coverage_threshold_tf --coverage_threshold_tf_diamond --csv_buffer_size --csv_buffer_size_dbsub --db_dir --e_value_threshold --e_value_threshold_dbcan --e_value_threshold_dbsub --e_value_threshold_stp --e_value_threshold_tc --e_value_threshold_tf --e_value_threshold_tf_diamond --enable_memory_monitoring --enable_memory_monitoring_dbsub --env --evalue_cutoff --extend_bp --extend_gene_count --extend_mode --extra_pair_type --extra_pair_type_num --feature_type --fungi --gff_type --hmmcov --hmmevalue --identity_cutoff --input_gff --input_raw_data --large --large_dbsub --large_input_threshold_mb --large_input_threshold_mb_dbsub --log-file --log-level --max_memory_usage --max_memory_usage_dbsub --max_retries --max_retries_dbsub --memory_safety_factor --memory_safety_factor_dbsub --methods --min_cluster_genes --min_core_cazyme --mode --no-enable_memory_monitoring --no-enable_memory_monitoring_dbsub --no-fungi --no-large --no-large_dbsub --no-prokaryotic --no-use_null_genes --num_null_gene --num_of_domains_substrate_cutoff --num_of_protein_substrate_cutoff --odbcan_sub --odbcanpul --out --output_dir --prodigal-gff-streaming --prodigal-streaming-threshold-mb --prokaryotic --pul --rerun --substrate_scors --threads --total_pair_num --uniq_pul_gene_hit_num --uniq_query_cgc_gene_num --use_distance --use_null_genes --verbose --verbose_option --workdir -bsc -cov -cpn -env -ept -eptn -evalue -hmmcov -hmmevalue -iden -ndsc -npsc -o -odbcan_sub -odbcanpul -rerun -subs -tpn -upghn -uqcgn -v -w

run_dbcan-gff_process command line option --coverage_threshold_peptidase --coverage_threshold_stp --coverage_threshold_sulfatase --coverage_threshold_tc --coverage_threshold_tf --coverage_threshold_tf_diamond --db_dir --e_value_threshold_peptidase --e_value_threshold_stp --e_value_threshold_sulfatase --e_value_threshold_tc --e_value_threshold_tf --e_value_threshold_tf_diamond --fungi --gff_type --input_gff --log-file --log-level --no-fungi --no-prokaryotic --output_dir --prodigal-gff-streaming --prodigal-streaming-threshold-mb --prokaryotic --threads --verbose -v run_dbcan-Pfam_null_cgc command line option --coverage_threshold_pfam --db_dir --e_value_threshold_pfam --log-file --log-level --null_from_gff --output_dir --run_pfam --threads --verbose -v run_dbcan-substrate_prediction command line option --bitscore_cutoff --CAZyme_pair_num --coverage_cutoff --db_dir --env --evalue_cutoff --extra_pair_type --extra_pair_type_num --hmmcov --hmmevalue --identity_cutoff --input_raw_data --log-file --log-level --mode --num_of_domains_substrate_cutoff --num_of_protein_substrate_cutoff --odbcan_sub --odbcanpul --out --output_dir --pul --rerun --substrate_scors --total_pair_num --uniq_pul_gene_hit_num --uniq_query_cgc_gene_num --verbose --workdir -bsc -cov -cpn -env -ept -eptn -evalue -hmmcov -hmmevalue -iden -ndsc -npsc -o -odbcan_sub -odbcanpul -rerun -subs -tpn -upghn -uqcgn -v -w