help with ref_map.pl options

[JS]

Hi all,

I'm quite new to STACKS and mysql. Pardon me if my doubts are incredibly basic or if did not catch up with the installation and running of stacks.

I'm currently working on the latest release stacks2.0. Initially tried working with Stacks2beta9 and stacks2beta10 (upgraded as and when new releases appeared in the last few days)

But when I type ref.map.pl -h in my terminal,

I get to see this (pasted below), instead of what is described in this link ( http://catchenlab.life.illinois.edu/stacks/comp-v1/ref_map.php ). I don't get to see the options for enabling database interaction and when I run ref_map.pl with -B option I get a reply that "Unknown command line option: '-B'".

Am I working with a wrong file/wrapper/folder?? Did I miss/skip anything during up-gradation/installation??

..Data/ngs/stacks-2.0$      ref_map.pl --samples ./ref_map_in/ -o ./ref_map_out/ -T 4 -O popmap -B refmap_radtags -b 1 -D 3mstk -X "populations:--fstats"

Unknown command line option: '-B'
ref_map.pl 2.0
ref_map.pl --samples dir --popmap path [-s spacer] [--paired] -o dir [-X prog:"opts" ...]

  Input/Output files:
    --samples: path to the directory containing the samples BAM (or SAM) alignment files.
    --popmap: path to a population map file (format is "<name> TAB <pop>", one sample per line).
    s: spacer for file names: by default this is empty and the program looks for files
       named 'SAMPLE_NAME.bam'; if this option is given the program looks for files
       named 'SAMPLE_NAME.SPACER.bam'.
    o: path to an output directory.
    --unpaired: ignore read pairing (for ddRAD; treat READ2's as if they were READ1's)
    --ignore-pe-reads: ignore paired-end reads even if present in the input

  General options:
    X: additional options for specific pipeline components, e.g. -X "populations: -p 3 -r 0.50"
    T: the number of threads/CPUs to use (default: 1).
    d: Dry run. Do not actually execute anything, just print the individual pipeline commands
       that would be executed.

  SNP model options:
    --var-alpha: significance level at which to call variant sites (for gstacks; default: 0.05).
    --gt-alpha: significance level at which to call genotypes (for gstacks; default: 0.05).

  Miscellaneous:
    --time-components (for benchmarking)

thanks
JS

[Nicolas Rochette]

Hi Jan,

http://catchenlab.life.illinois.edu/stacks/comp-v1/ref_map.php is for Stacks v1, the correct page for you is http://catchenlab.life.illinois.edu/stacks/comp/ref_map.php instead.

Nicolas

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[JS]

Hi Nicolas,

Thanks a lot for the mail and now I understand that there is not database for stacks 2.0 and interfacing with Mysql is dropped in all perl wrapper scripts.

JS

[Heather Tuttle]

Hello,

I am trying to use the ref_map.pl wrapper and gstacks is running fine.  I am having problems with populations.  See the log file attached. 

Any help would be great,

Heather