diff --git a/README.md b/README.md index 45af74b..ba85409 100644 --- a/README.md +++ b/README.md @@ -519,7 +519,7 @@ classify [OPTIONS] --index-filename --taxonomy-filename : Path to the Kraken 2 taxonomy file. This file contains taxonomic information used for classification. * -o, --options-filename : Path to the Kraken 2 options file. This file includes additional configuration options for Kraken 2. * -T, --confidence-threshold : Sets the confidence score threshold for classification. Sequences with a confidence score below this threshold will not be * classified. The default value is 0.0. -* -p, --num-threads : Specifies the number of threads to use for processing. Increasing the number of threads can speed up the classification process. The default is 1. +* -p, --num-threads : Specifies the number of threads to use for processing. Increasing the number of threads can speed up the classification process. The default is 10. * -g, --minimum-hit-groups : The minimum number of hit groups required for a classification call. The default is 2. * -P, --paired-end-processing: Enables processing of paired-end reads. This option should be used if your input files contain paired-end sequence data. * -S, --single-file-pairs: Indicates that pairs with mates are located in the same file. This option is relevant for paired-end processing. diff --git a/kr2r/src/args.rs b/kr2r/src/args.rs index e5f5823..dcf429a 100644 --- a/kr2r/src/args.rs +++ b/kr2r/src/args.rs @@ -91,7 +91,7 @@ pub struct ClassifyArgs { )] pub minimum_quality_score: i32, - /// The number of threads to use, default is 1. + /// The number of threads to use, default is 10. #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)] pub num_threads: i32, diff --git a/kr2r/src/bin/classify.rs b/kr2r/src/bin/classify.rs index 6b49842..1806d1b 100644 --- a/kr2r/src/bin/classify.rs +++ b/kr2r/src/bin/classify.rs @@ -49,8 +49,8 @@ struct Args { // /// Enable quick mode for faster processing. // #[clap(short = 'q', long = "quick-mode", action)] // quick_mode: bool, - /// The number of threads to use, default is 1. - #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 1)] + /// The number of threads to use, default is 10. + #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)] num_threads: i32, /// The minimum number of hit groups needed for a call. diff --git a/kr2r/src/bin/splitr.rs b/kr2r/src/bin/splitr.rs index 0fddb32..1fbf428 100644 --- a/kr2r/src/bin/splitr.rs +++ b/kr2r/src/bin/splitr.rs @@ -52,7 +52,7 @@ pub struct Args { )] pub minimum_quality_score: i32, - /// The number of threads to use, default is 1. + /// The number of threads to use, default is 10. #[clap(short = 'p', long = "num-threads", value_parser, default_value_t = 10)] pub num_threads: i32,