Please provide option of threads to srprism mkindex for the step of - Making host genome index for bmtagger

[ShevchenkoAlla]

Hello,
I am tryig to follow your instructions for Making host genome index for bmtagger

Your suggestion dont have threads option

srprism mkindex -i hg38.fa -o hg38.srprism -M 100000

Could you be so kind to add it as an option,
I have tried --threads, --thread, -t, -T - it's says unrecognised argument

I can't use it without specifing the number of threads
And I can't find the solution in google...

checking the options didn't helped also, Is it working on a single thread?

srprism mkindex --help

Fast Short Read Aligner

version 2.4.24-alpha

USAGE:

srprism cmd [--trace-level <min_level>] [--log-file <file-name>] [--input <input-file(s)>] [--input-list <file-name>] [--alt-loc <file-name>] [--output <output-stream>] [--input-format <format-name>] [--input-compression <compression-type>] [--output-format <format-name>] [--memory <megabytes>] [--seg-letters <bases>] [--al-extend <bases>]

COMMON PARAMETERS:

    cmd [required]

        Action to perform. Possible values are:

            * help           - get usage help;

            * search         - search for occurrences of the queries in 
                the database;

            * mkindex        - create index from a source database.

    --trace-level <min_level> [default: warning]

        Minimum message level to report to the log stream. Possible 
        values are "debug", "info", "warning", "error", "quiet".

    --log-file <file-name> [optional]

        File for storing diagnostic messages. Default is standard 
        error.

MKINDEX PARAMETERS:

    --input|-i <input-file(s)> [optional]

        Source database (may be a comma-separated list of file names). 
        This options takes precedence over --input-list.

    --input-list|-l <file-name> [optional]

        Name of the file containing a list of input file names, one 
        name per line.

    --alt-loc|-a <file-name> [optional]

        Name of the alternative loci specification file.

    --output|-o <output-stream> [required]

        Base name for generated database index files.

    --input-format|-F <format-name> [default: fasta]

        The input format name. The possible values are "fasta", 
        "fastq", "cfasta", "cfastq".

    --input-compression <compression-type> [default: auto]

        Compression type used for input. The possible values are 
        "auto" (default), "none", "gzip", and "bzip2". If the value 
        given is "auto" then the type of compression is guessed from 
        the file extension.

    --output-format|-O <format-name> [default: standard]

        The output format name. The possible values are "standard".

    --memory|-M <megabytes> [default: 2048]

        Do not use more than this many megabytes of memory for 
        internal dynamic data structures. This number does not include 
        the footprint of the executable code, static data, or stack.

    --seg-letters <bases> [default: 8192]

        Number of letters in sequence store segment. It is recommended 
        that this value is set to less than half of length of a 
        typical sequence in the reference database. Each reference 
        sequence occupies at least one segment and the sequence store 
        can store at most 2^32 - 1 bases. If the reference has a large 
        number of very short sequence, decreasing this value can help 
        to pack more sequences into the sequence store and optimize 
        memory usage.

    --al-extend <bases> [default: 2000]

        Number of reference bases by which an alternate locus is 
        extended to the left (right) in the case of non-fuzzy left 
        (right) end.

options_parser.cpp:239 [2] key error (unknown key help)
ERROR: options_parser.cpp:239 [2] key error (unknown key help) srprism.cpp:850
(metawrap-env)

I would appreciate any help,
Thanks

Best,
Alla