error in Genome Mepping by BWA tools in Linux
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15 months ago
$ gmap_build -D:\btau8refflat.gtf
Unknown option: D:btau8refflat.gtf
-k flag not specified, so building main hash table with default 15-mers
-j flag not specified, so building regional hash tables with default 6-mers

gmap_build: Builds a gmap database for a genome to be used by GMAP or GSNAP.
Part of GMAP package, version 2021-12-17.

Usage: gmap_build [options...] -d <genome> [-c <transcriptome> -T <transcript_fasta>] <genome_fasta_files>

You are free to name <genome> and <transcriptome> as you wish.  You
will use the same names when performing alignments subsequently using

Note: If adding a transcriptome to an existing genome, then there is
no need to specify the genome_fasta_files.  This way you can add
transcriptome information to an existing genome database.

    -D, --dir=STRING          Destination directory for installation (defaults to gmapdb
                                directory specified at configure time)
    -d, --genomedb=STRING     Genome name (required)

    -n, --names=STRING        Substitute names for contigs, provided in a file.
        The file can have two formats:
    1.  A file with one column per line, with each line
        corresponding to a FASTA file, in the order given to
        gmap_build.  The chromosome name for each FASTA file will
        be replaced with the desired chromosome name in the file.
        Every chromosome in the FASTA must have a corresponding line
        in the file.  This is useful if you want to rename chromosomes
        with a systematic numbering pattern.

    2.  A file with two columns per line, separated by white
        space.  In each line, the original FASTA chromosome name
        should be in column 1 and the desired chromosome name
        will be in column 2.

        The meaning of file format 2 depends on whether
        --limit-to-names is specified.  If so, the genome build will
        be limited to those chromosomes in this file.  Otherwise,
        all chromosomes in the FASTA file will be included,
        but only those chromosomes in this file will be re-named, which
        provides an easy way to change just a few chromosome names.

    This file can be combined with the --sort=names option, in
    which the order of chromosomes is that given in the file.  In
    this case, every chromosome must be listed in the file, and
    for chromosome names that should not be changed, column 2 can
    be blank (or the same as column 1).  The option of a blank
    column 2 is allowed only when specifying --sort=names,
    because otherwise, the program cannot distinguish between a
    1-column and 2-column names file.

-L, --limit-to-names      Determines whether to limit the genome build to the lines listed
                          in the --names file.  You can limit a genome build to certain
                          chromosomes with this option, plus a --names file that either
                          renames chromosomes, or lists the same names in both columns for
                          the desired chromosomes.

-k, --kmer=INT            k-mer value for genomic index (allowed: 15 or less, default is 15)
-q INT                    sampling interval for genomoe (allowed: 1-3, default 3)

-s, --sort=STRING         Sort chromosomes using given method:
                            none - use chromosomes as found in FASTA file(s) (default)
                            alpha - sort chromosomes alphabetically (chr10 before chr 1)
                            numeric-alpha - chr1, chr1U, chr2, chrM, chrU, chrX, chrY
                            chrom - chr1, chr2, chrM, chrX, chrY, chr1U, chrU
                            names - sort chromosomes based on file provided to --names flag

-g, --gunzip              Files are gzipped, so need to gunzip each file first
-E, --fasta-pipe=STRING   Interpret argument as a command, instead of a list of FASTA files
-Q, --fastq               Files are in FASTQ format
-R, --revcomp             Reverse complement all contigs
-w INT                    Wait (sleep) this many seconds after each step (default 2)

-o, --circular=STRING     Circular chromosomes (either a list of chromosomes separated
                            by a comma, or a filename containing circular chromosomes,
                            one per line).  If you use the --names feature, then you
                            should use the substitute name of the chromosome, not the
                            original name, for this option.  (NOTE: This behavior is different
                            from previous versions, and starts with version 2020-10-20.)

-2, --altscaffold=STRING  File with alt scaffold info, listing alternate scaffolds,
                            one per line, tab-delimited, with the following fields:
                            (1) alt_scaf_acc, (2) parent_name, (3) orientation,
                            (4) alt_scaf_start, (5) alt_scaf_stop, (6) parent_start, (7) parent_end.

-e, --nmessages=INT       Maximum number of messages (warnings, contig reports) to report (default 50)

Options for older genome formats: -M, --mdflag=STRING Use MD file from NCBI for mapping contigs to chromosomal coordinates

-C, --contigs-are-mapped  Find a chromosomal region in each FASTA header line.
                            Useful for contigs that have been mapped
                            to chromosomal coordinates.  Ignored if the --mdflag is provided.

Options for transcriptome-guided alignment: -c, --transcriptomedb=STRING Transcriptome name

-T, --transcripts=FILE    FASTA file containing transcripts (required if specifying

-t, --nthreads=INT        Number of threads for GMAP alignment of transcripts to genome
                            (default 8)

Must specify genome database name with -d flag. at /usr/bin/gmap_build line 69.

gmap NGS • 1.2k views
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No need to paste that all. A command line, the error and a wrotten sentence wouldn've been better. Are you on Windows?

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yes i am on window

Entering edit mode
kuldeep@DESKTOP-2BCQVVC:~$ gmap_build -d btau8 bosTau8.fa
-k flag not specified, so building main hash table with default 15-mers
-j flag not specified, so building regional hash tables with default 6-mers
Destination directory not defined with -D flag, so writing files under /var/cache/gmap
Not sorting chromosomes.  To sort chromosomes other ways, use the -s flag.
Creating files in directory /var/cache/gmap/btau8
mkdir: cannot create directory ‘/var/cache/gmap/btau8’: Permission denied
mkdir: cannot create directory ‘/var/cache/gmap/btau8’: Permission denied
chmod: cannot access '/var/cache/gmap/btau8/btau8.maps': No such file or directory
Could not create /var/cache/gmap/btau8.sources at /usr/bin/gmap_build line 221.
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This is a permission error unrelated to BWA. Your environment doesn't have the permission to write.

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How can i Resolve it

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learn to read the error messages:

Destination directory not defined with -D flag, so writing files under /var/cache/gmap

it tells you that you have not defined a cache directory and it picked one by default, but later it turns out it can't write there

Entering edit mode
15 months ago

the command is incorrect:

gmap_build -D:\btau8refflat.gtf

Under linux you cannot use colon : characters as paths, those characters only work on Windows to specify drives


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