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config.yaml
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config.yaml
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###################################################################################################
# search configuration - the parameters in this section affect results
##################################################
# general
# batches to consider during search
batches: "data/batches_2m.txt"
##################################################
##################################################
# kmer matching
# proportion of kmer presence between the query and the reference for matching, value between 0.00 and 1.00.
# E.g.: if this value is 0.7, then at least 70% of the query kmers must be present in a reference to match it.
# Lower values mean more matches and being able to recover partial hits, but also incurs into more spurious matches.
# Spurious matches just affect performance and not results - they are filtered out in the alignment phase.
# E.g. for plasmid search we recommend cobs_kmer_thres: 0.33
# Higher values mean less but more accurate matches and faster pipeline execution, but can incur into missing matches.
# E.g. for gene search we recommend cobs_kmer_thres: 0.7
cobs_kmer_thres: 0.7
# number of best kmer matching hits to keep for each query record (in case of tie, all equivalent hits are included too)
nb_best_hits: 1000
##################################################
##################################################
# alignment
# minimap2 preset. Can be:
# map-pb/map-ont: PacBio/Nanopore vs reference mapping
# ava-pb/ava-ont: PacBio/Nanopore read overlap
# asm5/asm10/asm20: asm-to-ref mapping, for ~0.1/1/5% sequence divergence
# splice: long-read spliced alignment
# sr: genomic short-read mapping
minimap_preset: "sr"
# other minimap2 params
minimap_extra_params: "--eqx"
##################################################
###################################################################################################
###################################################################################################
# performance configuration - the parameters in this section does NOT affect results, just performance
##################################################
# general
# overall number of threads to use in the pipeline, an integer number (e.g. 8 for 8 threads) or "all" (to use all threads)
threads: 8
# maximum RAM to use in GB - this should be at most 80% of your max RAM
# note: if you use more than your available RAM, constant page swapping will happen and the pipeline will severely
# slow down.
# if index_load_mode == mmap-disk, then this parameter is ignored as the OS will manage RAM usage
max_ram_gb: 15
##################################################
##################################################
# kmer matching
# number of threads when running COBS kmer matching
# allowed values are:
# auto: sets cobs_threads automatically, proportional to the amount of RAM used
# auto(N): same as auto, but the maximum number of threads is N, where N is an integer > 0
# N: sets cobs_threads to a fixed value N, where N is an integer > 0 (note: too many might limit the pipeline parallelism)
# WARNING: this parameter MUST BE SET to a fixed int value when running on a cluster
cobs_threads: 4
# specify how to load the kmer index. Options are:
# 1. mem-stream : default and preferred. With this mode, the pipeline extracts the compressed kmer index and streams
# it directly into COBS, which saves it completely in RAM. This mode uses the least filesystems operations
# possible, which is usually the bottleneck of this pipeline if your filesystem is slow.
# If this option is set, then parameters keep_cobs_indexes and decompression_dir are ignored.
# 2. mem-disk : this mode extracts the compressed kmer index to the disk, and then COBS loads it completely to the RAM.
# Can be an option if your filesystem is very fast. Another reason to use this mode is to speed up
# subsequent searches as the kmer indexes will be already decompressed, but that also requires parameter
# keep_cobs_indexes to be set to True, and will use lots of disk space.
# 3. mmap-disk : this mode extracts the compressed kmer index to the disk, and then COBS just loads parts of it on demand.
# This can be done if you don't have enough RAM to run the pipeline, but can incur huge slowdowns, especially
# if your filesystem is slow.
# If this mode is selected, then the parameter max_ram_gb is ignored.
index_load_mode: mem-stream
# maximum number of I/O-heavy threads. Use this to control the amount of filesystem I/O to not overflow the filesystem.
# it can control the amount of xz-decompression and COBS jobs (if index_load_mode == mmap-disk) that are run simultaneously.
# in more details, this parameter controls how many I/O-heavy threads can run simultaneously.
# I/O-heavy threads include:
# * 1 thread for xz-decompression of COBS kmer indexes;
# * 1 thread for each COBS process if index_load_mode is mmap-disk
max_io_heavy_threads: 5
##################################################
##################################################
# alignment
# number of threads when running minimap2 (note: too many might limit the pipeline parallelism)
minimap_threads: 1
# prefer use pipe when running minimap (note: switch this to False only if you are on *Linux* and you have a very fast filesystem)
prefer_pipe: True
##################################################
###################################################################################################
###################################################################################################
# misc configuration
# keep or not the decompressed COBS indexes. If kept, can speed up subsequent searches but will take much more disk
# space, as the decompressed indexes won't be cleaned up.
# if index_load_mode == mem-stream, then this parameter is ignored
keep_cobs_indexes: False
# directory to store the COBS decompressed indexes. Can be used to put the decompressed indexes in an external
# or large filesystem capable of holding them. If not defined, defaults to "intermediate/00_cobs"
# decompression_dir: cobs_decompressed_indexes
###################################################################################################