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#<< MiGA::TaxIndex
#<< MiGA::Taxonomy
CITATION MiGA::MiGA
CITATION_ARRAY MiGA::MiGA
DEBUG MiGA::MiGA
DEBUG_OFF MiGA::MiGA
DEBUG_ON MiGA::MiGA
DEBUG_TRACE_OFF MiGA::MiGA
DEBUG_TRACE_ON MiGA::MiGA
DISTANCE_TASKS MiGA::Project
EXECS MiGA::Cli
FILE_REGEXP MiGA::Cli
FULL_VERSION MiGA::MiGA
INCLADE_TASKS MiGA::Project
INFO_FIELDS MiGA::Dataset
INPUT_TYPES MiGA::Cli::Action::Add
KNOWN_RANKS MiGA::Taxonomy
KNOWN_TYPES MiGA::Dataset
KNOWN_TYPES MiGA::Project
LONG_RANKS MiGA::Taxonomy
LONG_VERSION MiGA::MiGA
OPERATIONS MiGA::Cli::Action::Doctor
OPTIONS MiGA::Dataset
OPTIONS MiGA::Project
PREPROCESSING_TASKS MiGA::Dataset
RESULT_DIRS MiGA::Project
RESULT_DIRS MiGA::Result
RESULT_DIRS MiGA::Dataset
TASK_ALIAS MiGA::Cli
TASK_DESC MiGA::Cli
UNIVERSE MiGA::RemoteDataset
VERSION MiGA::MiGA
VERSION_DATE MiGA::MiGA
#[] MiGA::Metadata
#[] MiGA::Cli
#[] MiGA::Result
#[] MiGA::Taxonomy
#[]= MiGA::Metadata
#[]= MiGA::Result
#[]= MiGA::Cli
aai_path MiGA::TaxDist
aai_pvalues MiGA::TaxDist
aai_taxtest MiGA::TaxDist
#action MiGA::Cli
#activate! MiGA::Dataset
#active? MiGA::Common::WithDaemon
#active? MiGA::Dataset
#active? MiGA::Project
#add_alternative MiGA::Taxonomy
#add_child MiGA::TaxIndexTaxon
#add_dataset MiGA::Project::Dataset
#add_dataset MiGA::TaxIndexTaxon
#add_file MiGA::Result
#add_files MiGA::Result
#add_hook MiGA::Common::Hooks
#add_metadata MiGA::Cli::ObjectsHelper
#add_result MiGA::Common::WithResult
#advance MiGA::Cli
#advance MiGA::MiGA
#alive_file MiGA::Common::WithDaemon
#alive_file MiGA::Common::WithDaemonClass
#all_datasets MiGA::TaxIndexTaxon
#all_options MiGA::Common::WithOption
#alternative MiGA::Taxonomy
#argv MiGA::Cli
#ask_user MiGA::Cli
#assert_has_option MiGA::Common::WithOption
#assert_valid_option_value MiGA::Common::WithOption
#banner MiGA::Cli::OptHelper
#bypass_maintenance? MiGA::Daemon::Base
#call_cli MiGA::Cli::Action::Wf
#cannid MiGA::Cli::Action::TaxDist
#check_additional_files MiGA::Cli::Action::Init::FilesHelper
#check_bidir MiGA::Cli::Action::Doctor::Distances
#check_cds MiGA::Cli::Action::Doctor::Operations
#check_configuration_script MiGA::Cli::Action::Init::FilesHelper
#check_datasets MiGA::Daemon
#check_db MiGA::Cli::Action::Doctor::Distances
#check_directories MiGA::Lair
#check_dist MiGA::Cli::Action::Doctor::Distances
#check_dist_eval MiGA::Cli::Action::Doctor::Base
#check_dist_fix MiGA::Cli::Action::Doctor::Base
#check_dist_recompute MiGA::Cli::Action::Doctor::Base
#check_ess MiGA::Cli::Action::Doctor::Operations
#check_files MiGA::Cli::Action::Doctor::Operations
#check_mts MiGA::Cli::Action::Doctor::Operations
#check_mytaxa_database MiGA::Cli::Action::Init::FilesHelper
#check_mytaxa_scores MiGA::Cli::Action::Init::FilesHelper
#check_phyla_lite MiGA::Cli::Action::Init::FilesHelper
#check_project MiGA::Daemon
#check_rdp_classifier MiGA::Cli::Action::Init::FilesHelper
#check_sqlite3_database MiGA::Cli::Action::Doctor::Databases
#check_start MiGA::Cli::Action::Doctor::Operations
#check_status MiGA::Cli::Action::Doctor::Operations
#check_tax MiGA::Cli::Action::Doctor::Operations
#children MiGA::TaxIndexTaxon
#clade? MiGA::Project
#clean! MiGA::Result
#clean? MiGA::Result
#clean_fasta_file MiGA::Common::Format
#cleanup MiGA::Cli::Action::Wf
#cleanup_distances! MiGA::Dataset::Result
#cli MiGA::Cli::Action
#cli_filters MiGA::Cli::Action::Download::Base
#cli_name_modifiers MiGA::Cli::Action::Download::Gtdb
#cli_name_modifiers MiGA::Cli::Action::Download::Ncbi
#cli_save_actions MiGA::Cli::Action::Download::Base
#cli_task_flags MiGA::Cli::Action::Download::Gtdb
#cli_task_flags MiGA::Cli::Action::Download::Ncbi
#close_rc_file MiGA::Cli::Action::Init::FilesHelper
#closest_relatives MiGA::Dataset
#complete MiGA::Cli::Action::Generic
#complete MiGA::Cli::Action
#complete MiGA::Cli::Action::GetDb
#compute_stats MiGA::Result::Stats
#configure_bash_daemon MiGA::Cli::Action::Init::DaemonHelper
#configure_daemon MiGA::Cli::Action::Init::DaemonHelper
#configure_qsub_msub_daemon MiGA::Cli::Action::Init::DaemonHelper
#configure_slurm_daemon MiGA::Cli::Action::Init::DaemonHelper
#configure_ssh_daemon MiGA::Cli::Action::Init::DaemonHelper
create MiGA::Result
#create MiGA::Result
#create MiGA::Project
#create MiGA::Metadata
#create_project MiGA::Cli::Action::Wf
#created MiGA::Metadata
#daemon MiGA::Common::WithDaemon
#daemon MiGA::Project
#daemon_first_loop MiGA::Lair
#daemon_first_loop MiGA::Daemon
#daemon_home MiGA::Daemon
daemon_home MiGA::Daemon
#daemon_home MiGA::Common::WithDaemonClass
#daemon_loop MiGA::Lair
#daemon_loop MiGA::Daemon
#daemon_name MiGA::Daemon
#daemon_name MiGA::Lair
#data MiGA::Result
#data MiGA::Cli
#data MiGA::Metadata
#dataset MiGA::Project::Dataset
#dataset_names MiGA::Project::Dataset
#dataset_names_hash MiGA::Project::Dataset
#datasets MiGA::Project::Dataset
#datasets MiGA::TaxIndexTaxon
#datasets MiGA::TaxIndex
#datasets_count MiGA::TaxIndexTaxon
#db MiGA::RemoteDataset
debug? MiGA::MiGA
debug_trace? MiGA::MiGA
#declare_alive MiGA::Common::WithDaemon
#declare_alive_loop MiGA::Common::WithDaemon
#declare_alive_pid MiGA::Common::WithDaemon
#default_hooks MiGA::Common::Hooks
#default_hooks MiGA::Project::Hooks
#default_hooks MiGA::Dataset::Hooks
#default_options MiGA::Common::WithDaemon
default_opts MiGA::SQLite
default_opts MiGA::Json
#default_opts_for_wf MiGA::Cli::Action::Wf
#defaults MiGA::Cli
#delete_alternative MiGA::Taxonomy
#dir MiGA::Result
#discard_excluded MiGA::Cli::Action::Download::Base
distribute MiGA::Parallel
#do_not_save MiGA::Project
#done_at MiGA::Result::Dates
#done_preprocessing? MiGA::Dataset::Result
#done_preprocessing? MiGA::Project::Dataset
download MiGA::RemoteDataset
#download MiGA::RemoteDataset::Download
#download_entries MiGA::Cli::Action::Download::Base
#download_file_ftp MiGA::Common::Net
download_rest MiGA::RemoteDataset
download_url MiGA::RemoteDataset
#each MiGA::Metadata
#each_daemon MiGA::Lair
#each_database_file MiGA::Cli::Action::Doctor::Databases
#each_dataset MiGA::Project::Dataset
#each_dataset_profile_advance MiGA::Project::Dataset
#each_file MiGA::Result
#each_project MiGA::Lair
#each_result MiGA::Common::WithResult
#empty_action MiGA::Cli::Action::Env
#empty_action MiGA::Cli::Action::Console
#empty_action MiGA::Cli::Action::GetDb
#empty_action MiGA::Cli::Action::Date
#empty_action MiGA::Cli::Action
#empty_action MiGA::Cli::Action::Init
#ensure_par MiGA::Cli
#ensure_type MiGA::Cli
exist? MiGA::Dataset
exist? MiGA::Result
exist? MiGA::Project
exist? MiGA::Metadata
#exit_cleanup MiGA::Daemon
#expect_files MiGA::Cli
#expect_operation MiGA::Cli
#file_path MiGA::Result
#files MiGA::Cli
#finalize_tasks MiGA::Cli::Action::Download::Base
#first_preprocessing MiGA::Dataset::Result
#flush! MiGA::Daemon
generate MiGA::Json
#generic_perform MiGA::Cli::Action::Download::Base
generic_transfer File
#get_gtdb_taxonomy MiGA::RemoteDataset
#get_job MiGA::Daemon
#get_metadata MiGA::RemoteDataset
#get_ncbi_taxid MiGA::RemoteDataset
#get_ncbi_taxonomy MiGA::RemoteDataset
#get_result MiGA::Common::WithResult
#get_type_status MiGA::RemoteDataset
#highest MiGA::Taxonomy
#hook__pull_result_hooks MiGA::Project::Hooks
#hook__pull_result_hooks MiGA::Dataset::Hooks
#hook_clear_run_counts MiGA::Dataset::Hooks
#hook_recalculate_status MiGA::Dataset::Hooks
#hook_run_cmd MiGA::Project::Hooks
#hook_run_cmd MiGA::Dataset::Hooks
#hook_run_lambda MiGA::Common::Hooks
#hooks MiGA::Common::Hooks
#ids MiGA::RemoteDataset
#ignore_task? MiGA::Project::Result
#ignore_task? MiGA::Dataset::Result
#import_dataset MiGA::Project::Dataset
#impose_limit MiGA::Cli::Action::Download::Base
#in? MiGA::Taxonomy
#in_loop MiGA::Common::WithDaemon
#inactivate! MiGA::Dataset
#inactivate! MiGA::Project::Result
#info MiGA::Dataset
#initialize MiGA::Result
#initialize MiGA::Project
#initialize MiGA::Cli::Action
#initialize MiGA::TaxIndexTaxon
#initialize MiGA::Cli
#initialize MiGA::SQLite
#initialize MiGA::TaxIndex
#initialize MiGA::Taxonomy
#initialize MiGA::Metadata
#initialize MiGA::Daemon
#initialize MiGA::RemoteDataset
#initialize MiGA::Dataset
#initialize MiGA::Lair
initialized? MiGA::MiGA
#interactive MiGA::Cli
#job_cmd MiGA::Daemon
#jobs_running MiGA::Daemon
#jobs_to_run MiGA::Daemon
json_create MiGA::Taxonomy
#key MiGA::Result::Source
#known_hosts MiGA::Common::Net
#l_say MiGA::Daemon
#last_alive MiGA::Common::WithDaemonClass
#last_alive MiGA::Common::WithDaemon
#latency MiGA::Daemon::Base
#launch MiGA::Cli::Action
#launch MiGA::Cli
#launch_daemon MiGA::Lair
#launch_daemon_proc MiGA::Common::WithDaemon
#launch_job MiGA::Daemon
#like_io? MiGA::MiGA
#list_requirements MiGA::Cli::Action::Init
load MiGA::Project
#load MiGA::Result
load MiGA::Cli::Action
#load MiGA::Metadata
load MiGA::Metadata
load MiGA::Result
#load MiGA::Project
#load_and_filter_datasets MiGA::Cli::ObjectsHelper
#load_dataset MiGA::Cli::ObjectsHelper
#load_project MiGA::Cli::ObjectsHelper
#load_project_or_dataset MiGA::Cli::ObjectsHelper
#load_result MiGA::Cli::ObjectsHelper
#load_status MiGA::Daemon
#load_tasks MiGA::Cli::Action::Download::Base
#lock_file MiGA::Metadata
#logfh MiGA::Daemon::Base
#loop_i MiGA::Common::WithDaemon
#lowest MiGA::Taxonomy
#maxjobs MiGA::Daemon::Base
#merge_bidir_tmp MiGA::Cli::Action::Doctor::Distances
#metadata MiGA::RemoteDataset
#metadata MiGA::Dataset
#metadata MiGA::Project
#miga_name String
#miga_name? String
#miga_say MiGA::Daemon
#miga_variables String
#multi? MiGA::Dataset
#multi? MiGA::Project
#name MiGA::Cli::Action::Generic
#name MiGA::Project
#name MiGA::Cli::Action
#name MiGA::TaxIndexTaxon
#name MiGA::Dataset
#namespace MiGA::Taxonomy
ncbi_asm_acc2id MiGA::RemoteDataset
#ncbi_asm_json_doc MiGA::RemoteDataset
ncbi_asm_rest MiGA::RemoteDataset
ncbi_gb_rest MiGA::RemoteDataset
ncbi_map MiGA::RemoteDataset
#next_distances MiGA::Project::Result
#next_host MiGA::Daemon
#next_inclade MiGA::Project::Result
#next_preprocessing MiGA::Dataset::Result
#next_task MiGA::Common::WithResult
#nodelist MiGA::Daemon::Base
#nonmulti? MiGA::Dataset
normalize_rank MiGA::Taxonomy
#num_suffix MiGA::MiGA
#open_rc_file MiGA::Cli::Action::Init::FilesHelper
#operation MiGA::Cli
#opt_common MiGA::Cli::OptHelper
#opt_filter_datasets MiGA::Cli::OptHelper
#opt_flag MiGA::Cli::OptHelper
#opt_object MiGA::Cli::OptHelper
#option MiGA::Common::WithOption
#option? MiGA::Common::WithOption
#option_by_default MiGA::Common::WithOption
#option_by_metadata MiGA::Common::WithOption
#option_from_string MiGA::Common::WithOption
#options MiGA::Lair
#options MiGA::Daemon
#opts MiGA::SQLite
#opts_for_wf MiGA::Cli::Action::Wf
#opts_for_wf_distances MiGA::Cli::Action::Wf
#outdated_fastaai_ess MiGA::Cli::Action::Doctor::Base
#output_file MiGA::Common::WithDaemon
parse MiGA::Json
#parse MiGA::Cli
#parse_cli MiGA::Cli::Action::TaxSet
#parse_cli MiGA::Cli::Action::Summary
#parse_cli MiGA::Cli::Action::Generic
#parse_cli MiGA::Cli::Action::Console
#parse_cli MiGA::Cli::Action::Archive
#parse_cli MiGA::Cli::Action::GetDb
#parse_cli MiGA::Cli::Action::Doctor
#parse_cli MiGA::Cli::Action::Daemon
#parse_cli MiGA::Cli::Action::Browse
#parse_cli MiGA::Cli::Action::Touch
#parse_cli MiGA::Cli::Action::Option
#parse_cli MiGA::Cli::Action::About
#parse_cli MiGA::Cli::Action::Files
#parse_cli MiGA::Cli::Action::Lair
#parse_cli MiGA::Cli::Action::Init
#parse_cli MiGA::Cli::Action::Date
#parse_cli MiGA::Cli::Action::Edit
#parse_cli MiGA::Cli::Action::Stats
#parse_cli MiGA::Cli::Action::Find
#parse_cli MiGA::Cli::Action::NcbiGet
#parse_cli MiGA::Cli::Action::New
#parse_cli MiGA::Cli::Action::Env
#parse_cli MiGA::Cli::Action::Get
#parse_cli MiGA::Cli::Action::Run
#parse_cli MiGA::Cli::Action::Add
#parse_cli MiGA::Cli::Action::Rm
#parse_cli MiGA::Cli::Action::Ls
#parse_cli MiGA::Cli::Action::Ln
#parse_cli MiGA::Cli::Action
#parse_cli MiGA::Cli::Action::ClassifyWf
#parse_cli MiGA::Cli::Action::QualityWf
#parse_cli MiGA::Cli::Action::AddResult
#parse_cli MiGA::Cli::Action::TaxIndex
#parse_cli MiGA::Cli::Action::PreprocWf
#parse_cli MiGA::Cli::Action::NextStep
#parse_cli MiGA::Cli::Action::TaxDist
#parse_cli MiGA::Cli::Action::TaxTest
#parse_cli MiGA::Cli::Action::GtdbGet
#parse_cli MiGA::Cli::Action::DerepWf
#parse_cli MiGA::Cli::Action::IndexWf
#partial_bidir_tmp MiGA::Cli::Action::Doctor::Distances
#path MiGA::Daemon
#path MiGA::Result
#path MiGA::Lair
#path MiGA::SQLite
#path MiGA::Metadata
#path MiGA::Project
#perform MiGA::Cli::Action::TaxSet
#perform MiGA::Cli::Action::Summary
#perform MiGA::Cli::Action::Generic
#perform MiGA::Cli::Action::Option
#perform MiGA::Cli::Action::Archive
#perform MiGA::Cli::Action::Console
#perform MiGA::Cli::Action::GetDb
#perform MiGA::Cli::Action::Daemon
#perform MiGA::Cli::Action::Stats
#perform MiGA::Cli::Action::Touch
#perform MiGA::Cli::Action::Browse
#perform MiGA::Cli::Action::Doctor
#perform MiGA::Cli::Action::About
#perform MiGA::Cli::Action::Files
#perform MiGA::Cli::Action::Lair
#perform MiGA::Cli::Action::Find
#perform MiGA::Cli::Action::Init
#perform MiGA::Cli::Action::Date
#perform MiGA::Cli::Action::Edit
#perform MiGA::Cli::Action::Get
#perform MiGA::Cli::Action::New
#perform MiGA::Cli::Action::Env
#perform MiGA::Cli::Action::Run
#perform MiGA::Cli::Action::Add
#perform MiGA::Cli::Action::Rm
#perform MiGA::Cli::Action::Ls
#perform MiGA::Cli::Action::Ln
#perform MiGA::Cli::Action
#perform MiGA::Cli::Action::ClassifyWf
#perform MiGA::Cli::Action::QualityWf
#perform MiGA::Cli::Action::AddResult
#perform MiGA::Cli::Action::TaxIndex
#perform MiGA::Cli::Action::TaxTest
#perform MiGA::Cli::Action::TaxDist
#perform MiGA::Cli::Action::NcbiGet
#perform MiGA::Cli::Action::NextStep
#perform MiGA::Cli::Action::PreprocWf
#perform MiGA::Cli::Action::GtdbGet
#perform MiGA::Cli::Action::DerepWf
#perform MiGA::Cli::Action::IndexWf
#pid_file MiGA::Common::WithDaemon
#ppn MiGA::Daemon::Base
#print MiGA::Cli
process MiGA::Parallel
#process_alive? MiGA::Common::WithDaemon
#profile_advance MiGA::Dataset::Result
#profile_datasets_advance MiGA::Project::Dataset
#project MiGA::Project::Result
#project MiGA::Result::Source
#project MiGA::Dataset
#project MiGA::Daemon
#project_path MiGA::Result::Source
#pull_hook MiGA::Common::Hooks
#purge! MiGA::Daemon
#puts MiGA::Cli
#query? MiGA::Dataset
#queue_job MiGA::Daemon
#queue_maintenance MiGA::Daemon
#rank MiGA::TaxIndexTaxon
#ranks MiGA::Taxonomy
rc_path MiGA::MiGA
#read_bidirectional MiGA::Cli::Action::Doctor::Base
#recalculate! MiGA::Result
#recalculate? MiGA::Result
#recalculate_status MiGA::Dataset::Status
#recalculate_tasks MiGA::Common::WithResult
#ref? MiGA::Dataset
#relative_dir MiGA::Result::Source
#relative_path MiGA::Result::Source
#reload_project MiGA::Daemon
#remote_connection MiGA::Common::Net
#remote_list MiGA::Cli::Action::Download::Ncbi
#remote_list MiGA::Cli::Action::Download::Gtdb
#remote_list_url MiGA::Cli::Action::Download::Ncbi
#remote_row_name MiGA::Cli::Action::Download::Ncbi
#remote_row_name MiGA::Cli::Action::Download::Gtdb
#remote_row_replicons MiGA::Cli::Action::Download::Ncbi
#remove! MiGA::Metadata
#remove! MiGA::Dataset
#remove! MiGA::Result
#reset MiGA::Taxonomy
#reset_action MiGA::Cli
#result MiGA::Common::WithResult
#result_base MiGA::Project::Result
#result_base MiGA::Dataset::Result
#result_dirs MiGA::Common::WithResult
#result_files_exist? MiGA::MiGA
#result_status MiGA::Dataset::Result
#results MiGA::Common::WithResult
#results_status MiGA::Dataset::Result
#root MiGA::TaxIndex
#root_path MiGA::Common::Path
#run MiGA::SQLite
#run MiGA::Common::WithDaemon
#run_block MiGA::SQLite
#run_cmd MiGA::Cli::Action::Doctor::Base
#run_cmd MiGA::Common::SystemCall
#run_cmd MiGA::Cli::Action::Init
#run_cmd_opts MiGA::Common::SystemCall
#run_daemon MiGA::Cli::Action::Wf
#run_r_cmd MiGA::Cli::Action::Init
#running_time MiGA::Result::Dates
#runopts MiGA::Daemon::Base
#runopts_for MiGA::Daemon::Base
#sanitize_cli MiGA::Cli::Action::Download::Ncbi
#sanitize_cli MiGA::Cli::Action::Download::Gtdb
#save MiGA::Dataset
#save MiGA::Project
#save MiGA::Result
#save MiGA::Metadata
#save! MiGA::Project
#save_bidirectional MiGA::Cli::Action::Doctor::Base
#save_entry MiGA::Cli::Action::Download::Base
#save_status MiGA::Daemon
#save_to MiGA::RemoteDataset
#saved_targets MiGA::Cli::Action::Doctor::Base
#say MiGA::MiGA
#say MiGA::Cli
#say MiGA::Daemon
#script_path MiGA::Common::Path
#seqs_length MiGA::Common::Format
#set_option MiGA::Common::WithOption
#show_log! MiGA::Daemon::Base
#show_log? MiGA::Daemon::Base
#show_summary! MiGA::Daemon::Base
#shutdown_when_done? MiGA::Daemon::Base
#skip_maintenance MiGA::Daemon::Base
#sorted_ranks MiGA::Taxonomy
#source MiGA::Result::Source
#start MiGA::Common::WithDaemon
#started_at MiGA::Result::Dates
#stats MiGA::Result::Stats
#status MiGA::Common::WithDaemon
#status MiGA::Dataset::Status
#stop MiGA::Common::WithDaemon
#summarize MiGA::Cli::Action::Wf
#table MiGA::Cli
#tabulate MiGA::Common::Format
#task MiGA::Cli
#task_description MiGA::Cli
#tax_str MiGA::TaxIndexTaxon
#taxa_by_rank MiGA::TaxIndex
#terminate MiGA::Common::WithDaemon
#terminate_daemon MiGA::Lair
#terminate_daemons MiGA::Lair
#terminate_file MiGA::Common::WithDaemon
#terminated_file MiGA::Common::WithDaemonClass
#terminated_file MiGA::Common::WithDaemon
#termination_file? MiGA::Common::WithDaemon
thread_enum MiGA::Parallel
#to_hash MiGA::TaxIndexTaxon
#to_json MiGA::TaxIndexTaxon
#to_json MiGA::TaxIndex
#to_json MiGA::Taxonomy
#to_json MiGA::Metadata
#to_s MiGA::Taxonomy
#to_tab MiGA::TaxIndex
#to_tab MiGA::TaxIndexTaxon
#transfer_metadata MiGA::Cli::Action::Wf
#type MiGA::Dataset
#type MiGA::Project
#universe MiGA::RemoteDataset
#unlink MiGA::Result
#unlink_dataset MiGA::Project::Dataset
#unlink_entries MiGA::Cli::Action::Download::Base
#unmiga_name String
#unregistered_datasets MiGA::Project::Dataset
#update_format_0 MiGA::Daemon
#update_metadata MiGA::RemoteDataset
#updated MiGA::Metadata
#verbosity MiGA::Daemon::Base
#why_ignore MiGA::Dataset::Result
#wrap_width String
#write_alive_file MiGA::Common::WithDaemon