$ emapper.py -h usage: emapper.py [-h] [-v] [--list_taxa] [--cpu NUM_CPU] [--mp_start_method {fork,spawn,forkserver}] [--resume] [--override] [-i FASTA_FILE] [--itype {CDS,proteins,genome,metagenome}] [--translate] [--annotate_hits_table SEED_ORTHOLOGS_FILE] [-c FILE] [--data_dir DIR] [--genepred {search,prodigal}] [--trans_table TRANS_TABLE_CODE] [--training_genome FILE] [--training_file FILE] [--allow_overlaps {none,strand,diff_frame,all}] [--overlap_tol FLOAT] [-m {diamond,mmseqs,hmmer,no_search,cache,novel_fams}] [--pident PIDENT] [--query_cover QUERY_COVER] [--subject_cover SUBJECT_COVER] [--evalue EVALUE] [--score SCORE] [--dmnd_algo {auto,0,1,ctg}] [--dmnd_db DMND_DB_FILE] [--sensmode {default,fast,mid-sensitive,sensitive,more-sensitive,very-sensitive,ultra-sensitive}] [--dmnd_iterate {yes,no}] [--matrix {BLOSUM62,BLOSUM90,BLOSUM80,BLOSUM50,BLOSUM45,PAM250,PAM70,PAM30}] [--dmnd_frameshift DMND_FRAMESHIFT] [--gapopen GAPOPEN] [--gapextend GAPEXTEND] [--block_size BLOCK_SIZE] [--index_chunks CHUNKS] [--outfmt_short] [--dmnd_ignore_warnings] [--mmseqs_db MMSEQS_DB_FILE] [--start_sens START_SENS] [--sens_steps SENS_STEPS] [--final_sens FINAL_SENS] [--mmseqs_sub_mat SUBS_MATRIX] [-d HMMER_DB_PREFIX] [--servers_list FILE] [--qtype {hmm,seq}] [--dbtype {hmmdb,seqdb}] [--usemem] [-p PORT] [--end_port PORT] [--num_servers NUM_SERVERS] [--num_workers NUM_WORKERS] [--timeout_load_server TIMEOUT_LOAD_SERVER] [--hmm_maxhits MAXHITS] [--report_no_hits] [--hmm_maxseqlen MAXSEQLEN] [--Z DB_SIZE] [--cut_ga] [--clean_overlaps none|all|clans|hmmsearch_all|hmmsearch_clans] [--no_annot] [--dbmem] [--seed_ortholog_evalue MIN_E-VALUE] [--seed_ortholog_score MIN_SCORE] [--tax_scope TAX_SCOPE] [--tax_scope_mode TAX_SCOPE_MODE] [--target_orthologs {one2one,many2one,one2many,many2many,all}] [--target_taxa LIST_OF_TAX_IDS] [--excluded_taxa LIST_OF_TAX_IDS] [--report_orthologs] [--go_evidence {experimental,non-electronic,all}] [--pfam_realign {none,realign,denovo}] [--md5] [--output FILE_PREFIX] [--output_dir DIR] [--scratch_dir DIR] [--temp_dir DIR] [--no_file_comments] [--decorate_gff DECORATE_GFF] [--decorate_gff_ID_field DECORATE_GFF_ID_FIELD] [--excel] options: -h, --help show this help message and exit -v, --version show version and exit. (default: False) --list_taxa List taxa available for --tax_scope/--tax_scope_mode, and exit (default: False) Execution Options: --cpu NUM_CPU Number of CPUs to be used. --cpu 0 to run with all available CPUs. (default: 1) --mp_start_method {fork,spawn,forkserver} Sets the python multiprocessing start method. Check https://docs.python.org/3/library/multiprocessing.html. Only use if the default method is not working properly in your OS. (default: spawn) --resume Resumes a previous emapper run, skipping results in existing output files. (default: False) --override Overwrites output files if they exist. By default, execution is aborted if conflicting files are detected. (default: False) Input Data Options: -i FASTA_FILE Input FASTA file containing query sequences (proteins by default; see --itype and --translate). Required unless -m no_search. (default: None) --itype {CDS,proteins,genome,metagenome} Type of data in the input (-i) file. (default: proteins) --translate When --itype CDS, translate CDS to proteins before search. When --itype genome/metagenome and --genepred search, translate predicted CDS from blastx hits to proteins. (default: False) --annotate_hits_table SEED_ORTHOLOGS_FILE Annotate TSV formatted table with 4 fields: query, hit, evalue, score. Usually, a .seed_orthologs file from a previous emapper.py run. Requires -m no_search. (default: None) -c FILE, --cache FILE File containing annotations and md5 hashes of queries, to be used as cache. Required if -m cache (default: None) --data_dir DIR Path to eggnog-mapper databases. By default, "data/" or the path specified in the environment variable EGGNOG_DATA_DIR. (default: None) Gene Prediction Options: --genepred {search,prodigal} This is applied when --itype genome or --itype metagenome. search: gene prediction is inferred from Diamond/MMseqs2 blastx hits. prodigal: gene prediction is performed using Prodigal. (default: search) --trans_table TRANS_TABLE_CODE This option will be used for Prodigal, Diamond or MMseqs2, depending on the mode. For Diamond searches, this option corresponds to the --query-gencode option. For MMseqs2 searches, this option corresponds to the --translation-table option. For Prodigal, this option corresponds to the -g/--trans_table option. It is also used when --translate, check https://biopython.org/docs/1.75/api/Bio.Seq.html#Bio.Seq.Seq.translate. Default is the corresponding programs defaults. (default: None) --training_genome FILE A genome to run Prodigal in training mode. If this parameter is used, Prodigal will run in two steps: firstly in training mode, and secondly using the training to analize the emapper input data. See Prodigal documentation about Traning mode for more info. Only used if --genepred prodigal. (default: None) --training_file FILE A training file from Prodigal training mode. If this parameter is used, Prodigal will run using this training file to analyze the emapper input data. Only used if --genepred prodigal. (default: None) --allow_overlaps {none,strand,diff_frame,all} When using 'blastx'-based genepred (--genepred search --itype genome/metagenome) this option controls whether overlapping hits are reported or not, or if only those overlapping hits in a different strand or frame are reported. Also, the degree of accepted overlap can be controlled with --overlap_tol. (default: none) --overlap_tol FLOAT This value (0-1) is the proportion such that if (overlap size / hit length) > overlap_tol, hits are considered to overlap. e.g: if overlap_tol is 0.0, any overlap is considered as such. e.g: if overlap_tol is 1.0, one of the hits must overlap entirely to consider that hits do overlap. (default: 0.0) Search Options: -m {diamond,mmseqs,hmmer,no_search,cache,novel_fams} diamond: search seed orthologs using diamond (-i is required). mmseqs: search seed orthologs using MMseqs2 (-i is required). hmmer: search seed orthologs using HMMER. (-i is required). no_search: skip seed orthologs search (--annotate_hits_table is required, unless --no_annot). cache: skip seed orthologs search and annotate based on cached results (-i and -c are required).novel_fams: search against the novel families database (-i is required). (default: diamond) Search filtering common options: --pident PIDENT Report only alignments above or equal to the given percentage of identity (0-100).No effect if -m hmmer. (default: None) --query_cover QUERY_COVER Report only alignments above or equal the given percentage of query cover (0-100).No effect if -m hmmer. (default: None) --subject_cover SUBJECT_COVER Report only alignments above or equal the given percentage of subject cover (0-100).No effect if -m hmmer. (default: None) --evalue EVALUE Report only alignments below or equal the e-value threshold. (default: 0.001) --score SCORE Report only alignments above or equal the score threshold. (default: None) Diamond Search Options: --dmnd_algo {auto,0,1,ctg} Diamond's --algo option, which can be tuned to search small query sets. By default, it is adjusted automatically. However, the ctg option should be activated manually. If you plan to search a small input set of sequences, use --dmnd_algo ctg to make it faster. (default: auto) --dmnd_db DMND_DB_FILE Path to DIAMOND-compatible database (default: None) --sensmode {default,fast,mid-sensitive,sensitive,more-sensitive,very-sensitive,ultra-sensitive} Diamond's sensitivity mode. Note that emapper's default is sensitive, which is different from diamond's default, which can be activated with --sensmode default. (default: sensitive) --dmnd_iterate {yes,no} --dmnd_iterate yes --> activates the --iterate option of diamond for iterative searches, from faster, less sensitive modes, up to the sensitivity specified with --sensmode. Available since diamond 2.0.11. --dmnd_iterate no --> disables the --iterate mode. (default: yes) --matrix {BLOSUM62,BLOSUM90,BLOSUM80,BLOSUM50,BLOSUM45,PAM250,PAM70,PAM30} Scoring matrix (default: None) --dmnd_frameshift DMND_FRAMESHIFT Diamond --frameshift/-F option. Not used by default. Recommended by diamond: 15. (default: None) --gapopen GAPOPEN Gap open penalty (default: None) --gapextend GAPEXTEND Gap extend penalty (default: None) --block_size BLOCK_SIZE Diamond -b/--block-size option. Default is the diamond's default. (default: None) --index_chunks CHUNKS Diamond -c/--index-chunks option. Default is the diamond's default. (default: None) --outfmt_short Diamond output will include only qseqid sseqid evalue and score. This could help obtain better performance, if also no --pident, --query_cover or --subject_cover thresholds are used. This option is ignored when the diamond search is run in blastx mode for gene prediction (see --genepred). (default: False) --dmnd_ignore_warnings Diamond --ignore-warnings option. It avoids Diamond stopping due to warnings (e.g. when a protein contains only ATGC symbols. (default: False) MMseqs2 Search Options: --mmseqs_db MMSEQS_DB_FILE Path to MMseqs2-compatible database (default: None) --start_sens START_SENS Starting sensitivity. (default: 3) --sens_steps SENS_STEPS Number of sensitivity steps. (default: 3) --final_sens FINAL_SENS Final sensititivy step. (default: 7) --mmseqs_sub_mat SUBS_MATRIX Matrix to be used for --sub-mat MMseqs2 search option. Default=default used by MMseqs2 (default: None) HMMER Search Options: -d HMMER_DB_PREFIX, --database HMMER_DB_PREFIX specify the target database for sequence searches. Choose among: euk,bact,arch, or a database loaded in a server, db.hmm:host:port (see hmm_server.py) (default: None) --servers_list FILE A FILE with a list of remote hmmpgmd servers. Each row in the file represents a server, in the format 'host:port'. If --servers_list is specified, host and port from -d option will be ignored. (default: None) --qtype {hmm,seq} Type of input data (-i). (default: seq) --dbtype {hmmdb,seqdb} Type of data in DB (-db). (default: hmmdb) --usemem Use this option to allocate the whole database (-d) in memory using hmmpgmd. If --dbtype hmm, the database must be a hmmpress-ed database. If --dbtype seqdb, the database must be a HMMER-format database created with esl-reformat. Database will be unloaded after execution. Note that this only works for HMMER based searches. To load the eggnog-mapper annotation DB into memory use --dbmem. (default: False) -p PORT, --port PORT Port used to setup HMM server, when --usemem. Also used for --pfam_realign modes. (default: 51700) --end_port PORT Last port to be used to setup HMM server, when --usemem. Also used for --pfam_realign modes. (default: 53200) --num_servers NUM_SERVERS When using --usemem, specify the number of servers to fire up.Note that cpus specified with --cpu will be distributed among servers and workers. Also used for --pfam_realign modes. (default: 1) --num_workers NUM_WORKERS When using --usemem, specify the number of workers per server (--num_servers) to fire up. By default, cpus specified with --cpu will be distributed among servers and workers. Also used for --pfam_realign modes. (default: 1) --timeout_load_server TIMEOUT_LOAD_SERVER Number of attempts to load a server on a specific port. If failed, the next numerical port will be tried. (default: 10) --hmm_maxhits MAXHITS Max number of hits to report (0 to report all). (default: 1) --report_no_hits Whether queries without hits should be included in the output table. (default: False) --hmm_maxseqlen MAXSEQLEN Ignore query sequences larger than `maxseqlen`. (default: 5000) --Z DB_SIZE Fixed database size used in phmmer/hmmscan (allows comparing e-values among databases). (default: 40000000) --cut_ga Adds the --cut_ga to hmmer commands (useful for Pfam mappings, for example). See hmmer documentation. (default: False) --clean_overlaps none|all|clans|hmmsearch_all|hmmsearch_clans Removes those hits which overlap, keeping only the one with best evalue. Use the "all" and "clans" options when performing a hmmscan type search (i.e. domains are in the database). Use the "hmmsearch_all" and "hmmsearch_clans" options when using a hmmsearch type search (i.e. domains are the queries from -i file). The "clans" and "hmmsearch_clans" and options will only have effect for hits to/from Pfam. (default: None) Annotation Options: --no_annot Skip functional annotation, reporting only hits. (default: False) --dbmem Use this option to allocate the whole eggnog.db DB in memory. Database will be unloaded after execution. (default: False) --seed_ortholog_evalue MIN_E-VALUE Min E-value expected when searching for seed eggNOG ortholog. Queries not having a significant seed orthologs will not be annotated. (default: 0.001) --seed_ortholog_score MIN_SCORE Min bit score expected when searching for seed eggNOG ortholog. Queries not having a significant seed orthologs will not be annotated. (default: None) --tax_scope TAX_SCOPE Fix the taxonomic scope used for annotation, so only speciation events from a particular clade are used for functional transfer. More specifically, the --tax_scope list is intersected with the seed orthologs clades, and the resulting clades are used for annotation based on --tax_scope_mode. Note that those seed orthologs without clades intersecting with --tax_scope will be filtered out, and won't annotated. Possible arguments for --tax_scope are: 1) A path to a file defined by the user, which contains a list of tax IDs and/or tax names. 2) The name of a pre-configured tax scope, whose source is a file stored within the 'eggnogmapper/annotation/tax_scopes/' directory By default, available ones are: 'auto' ('all'), 'auto_broad' ('all_broad'), 'all_narrow', 'archaea', 'bacteria', 'bacteria_broad', 'eukaryota', 'eukaryota_broad' and 'prokaryota_broad'.3) A comma-separated list of taxonomic names and/or taxonomic IDs, sorted by preference. An example of list of tax IDs would be 2759,2157,2,1 for Eukaryota, Archaea, Bacteria and root, in that order of preference. 4) 'none': do not filter out annotations based on taxonomic scope. (default: auto) --tax_scope_mode TAX_SCOPE_MODE For a seed ortholog which passed the filter imposed by --tax_scope, --tax_scope_mode controls which specific clade, to which the seed ortholog belongs, will be used for annotation. Options: 1) broadest: use the broadest clade. 2) inner_broadest: use the broadest clade from the intersection with --tax_scope. 3) inner_narrowest: use the narrowest clade from the intersection with --tax_scope. 4) narrowest: use the narrowest clade. 5) A taxonomic scope as in --tax_scope: use this second list to intersect with seed ortholog clades and use the narrowest (as in inner_narrowest) from the intersection to annotate. (default: inner_narrowest) --target_orthologs {one2one,many2one,one2many,many2many,all} defines what type of orthologs (in relation to the seed ortholog) should be used for functional transfer (default: all) --target_taxa LIST_OF_TAX_IDS Only orthologs from the specified comma-separated list of taxa and all its descendants will be used for annotation transference. By default, all taxa are used. (default: None) --excluded_taxa LIST_OF_TAX_IDS Orthologs from the specified comma-separated list of taxa and all its descendants will not be used for annotation transference. By default, no taxa is excluded. (default: None) --report_orthologs Output the list of orthologs found for each query to a .orthologs file (default: False) --go_evidence {experimental,non-electronic,all} Defines what type of GO terms should be used for annotation. experimental = Use only terms inferred from experimental evidence. non-electronic = Use only non- electronically curated terms (default: non-electronic) --pfam_realign {none,realign,denovo} Realign the queries to the PFAM domains. none = no realignment is performed. PFAM annotation will be that transferred as specify in the --pfam_transfer option. realign = queries will be realigned to the PFAM domains found according to the --pfam_transfer option. denovo = queries will be realigned to the whole PFAM database, ignoring the --pfam_transfer option. Check hmmer options (--num_servers, --num_workers, --port, --end_port) to change how the hmmpgmd server is run. (default: none) --md5 Adds the md5 hash of each query as an additional field in annotations output files. (default: False) Output options: --output FILE_PREFIX, -o FILE_PREFIX base name for output files (default: None) --output_dir DIR Where output files should be written (default: /data/work/Enrich/eggNOGmapper/db) --scratch_dir DIR Write output files in a temporary scratch dir, move them to the final output dir when finished. Speed up large computations using network file systems. (default: None) --temp_dir DIR Where temporary files are created. Better if this is a local disk. (default: /data/work/Enrich/eggNOGmapper/db) --no_file_comments No header lines nor stats are included in the output files (default: False) --decorate_gff DECORATE_GFF Add search hits and/or annotation results to GFF file from gene prediction of a user specified one. no = no GFF decoration at all. GFF file from blastx-based gene prediction will be created anyway. yes = add search hits and/or annotations to GFF file from Prodigal or blastx-based gene prediction. FILE = decorate the specified pre-existing GFF FILE. e.g. --decorage_gff myfile.gff You change the field interpreted as ID of the feature with --decorate_gff_ID_field. (default: no) --decorate_gff_ID_field DECORATE_GFF_ID_FIELD Change the field used in GFF files as ID of the feature. (default: ID) --excel Output annotations also in .xlsx format. (default: False) # Example usage: emapper.py \ --cpu 8 \ # 使用8个CPU核心 --mp_start_method forkserver \ # 多进程启动方法（避免内存泄漏） --data_dir /data/work/Enrich/eggNOGmapper/db \ # 数据库放在内存盘（加速） -o test \ # 输出文件基础名 --output_dir /data/work/Enrich/eggNOGmapper/output \ # 输出目录 --temp_dir /data/work/Enrich/eggNOGmapper/output \ # 临时文件目录 --override \ # 覆盖已有结果 -m diamond \ # 使用DIAMOND而不是HMMER（更快） --dmnd_ignore_warnings \ # 忽略DIAMOND警告 -i /data/work/Enrich/TM-1_V2.1.gene.pep.fa \ # 输入FASTA文件 --evalue 0.001 \ # E值阈值 --score 60 \ # 比特分数阈值 --pident 40 \ # 序列一致性阈值40% --query_cover 20 \ # 查询覆盖度20% --subject_cover 20 \ # 目标覆盖度20% --itype proteins \ # 输入类型为蛋白质 --tax_scope auto \ # 自动确定分类范围 --target_orthologs all \ # 报告所有直系同源基因 --go_evidence non-electronic \ # 只包含非电子注释的GO条目 --pfam_realign none \ # 不重新比对Pfam域 --report_orthologs \ # 报告直系同源基因列表 --decorate_gff yes \ # 生成GFF注释装饰文件 --excel # 生成Excel格式输出