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PROGRAM:

NAME


cmcalibrate - fit exponential tails for covariance model E-value determination

SYNOPSIS


cmcalibrate [options] cmfile

DESCRIPTION


cmcalibrate determines exponential tail parameters for E-value determination by generating
random sequences, searching them with the CM and collecting the scores of the resulting
hits. A histogram of the bit scores of the hits is fit to an exponential tail, and the
parameters of the fitted tail are saved to the CM file. The exponential tail parameters
are then used to estimate the statistical significance of hits found in cmsearch and
cmscan.

A CM file must be calibrated with cmcalibrate before it can be used in cmsearch or cmscan,
with a single exception: it is not necessary to calibrate CM files that include only
models with zero basepairs before running cmsearch.

cmcalibrate is very slow. It takes a couple of hours to calibrate a single average sized
CM on a single CPU. cmcalibrate will run in parallel on all available cores if Infernal
was built on a system that supports POSIX threading (see the Installation section of the
user guide for more information). Using <n> cores will result in roughly <n> -fold
acceleration versus a single CPU. MPI (Message Passing Interface) can be also be used for
parallelization with the --mpi option if Infernal was built with MPI enabled, but using
more than 161 processors is not recommended because increasing past 161 won't accelerate
the calibration. See the Installation seciton of the user guide for more information.

The --forecast option can be used to estimate how long the program will take to run for a
given cmfile on the current machine. To predict the running time on <n> processors with
MPI, additionally use the --nforecast <n> option.

The random sequences searched in cmcalibrate are generated by an HMM that was trained on
real genomic sequences with various GC contents. The goal is to have the GC distributions
in the random sequences be similar to those in actual genomic sequences.

Four rounds of searches and subsequent exponential tail fits are performed, one each for
the four different CM algorithms that can be used in cmsearch and cmscan: glocal CYK,
glocal Inside, local CYK and local Inside.

The E-values parameters determined by cmcalibrate are only used by the cmsearch and cmscan
programs. If you are not going to use these programs then do not waste time calibrating
your models.

OPTIONS


-h Help; print a brief reminder of command line usage and available options.

-L <x> Set the total length of random sequences to search to <x> megabases (Mb). By
default, <x> is 1.6 Mb. Increasing <x> will make the exponential tail fits more
precise and E-values more accurate, but will take longer (doubling <x> will roughly
double the running time). Decreasing <x> is not recommended as it will make the
fits less precise and the E-values less accurate.

OPTIONS FOR PREDICTING REQUIRED TIME AND MEMORY


--forecast
Predict the running time of the calibration of cmfile (with provided options) on
the current machine and exit. The calibration is not performed. The predictions
should be considered rough estimates. If multithreading is enabled (see
Installation section of user guide), the timing will take into account the number
of available cores.

--nforecast <n>
With --forecast, specify that <n> processors will be used for the calibration.
This might be useful for predicting the running time of an MPI run with <n>
processors.

--memreq
Predict the amount of required memory for calibrating cmfile (with provided
options) on the current machine and exit. The calibration is not performed.

OPTIONS CONTROLLING EXPONENTIAL TAIL FITS


--gtailn <x>
fit the exponential tail for glocal Inside and glocal CYK to the <n> highest scores
in the histogram tail, where <n> is <x> times the number of Mb searched. The
default value of <x> is 250. The value 250 was chosen because it works well
empirically relative to other values.

--ltailn <x>
fit the exponential tail for local Inside and local CYK to the <n> highest scores
in the histogram tail, where <n> is <x> times the number of Mb searched. The
default value of <x> is 750. The value 750 was chosen because it works well
empirically relative to other values.

--tailp <x>
Ignore the --gtailn and --ltailn prefixed options and fit the <x> fraction tail of
the histogram to an exponential tail, for all search modes.

OPTIONAL OUTPUT FILES


--hfile <f>
Save the histograms fit to file <f>. The format of this file is two space
delimited columns per line. The first column is the x-axis values of bit scores of
each bin. The second column is the y-axis values of number of hits per bin. Each
series is delimited by a line with a single character "&". The file will contain
one series for each of the four exponential tail fits in the following order:
glocal CYK, glocal Inside, local CYK, and local Inside.

--sfile <f>
Save survival plot information to file <f>. The format of this file is two space
delimited columns per line. The first column is the x-axis values of bit scores of
each bin. The second column is the y-axis values of fraction of hits that meet or
exceed the score for each bin. Each series is delimited by a line with a single
character "&". The file will contain three series of data for each of the four CM
search modes in the following order: glocal CYK, glocal Inside, local CYK, and
local Inside. The first series is the empirical survival plot from the histogram
of hits to the random sequence. The second series is the exponential tail fit to
the empirical distribution. The third series is the exponential tail fit if lambda
were fixed and set as the natural log of 2 (0.691314718).

--qqfile <f>
Save quantile-quantile plot information to file <f>. The format of this file is
two space delimited columns per line. The first column is the x-axis values, and
the second column is the y-axis values. The distance of the points from the
identity line (y=x) is a measure of how good the exponential tail fit is, the
closer the points are to the identity line, the better the fit is. Each series is
delimited by a line with a single character "&". The file will contain one series
of empirical data for each of the four exponential tail fits in the following
order: glocal CYK, glocal Inside, local CYK and local Inside.

--ffile <f>
Save space delimited statistics of different exponential tail fits to file <f>.
The file will contain the lambda and mu values for exponential tails fit to
histogram tails of different sizes. The fields in the file are labelled
informatively.

--xfile <f>
Save a list of the scores in each fit histogram tail to file <f>. Each line of
this file will have a different score indicating one hit existed in the tail with
that score. Each series is delimited by a line with a single character "&". The
file will contain one series for each of the four exponential tail fits in the
following order: glocal CYK, glocal Inside, local CYK, and local Inside.

OTHER OPTIONS


--seed <n>
Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero,
stochastic simulations will be reproducible; the same command will give the same
results. If <n> is 0, the random number generator is seeded arbitrarily, and
stochastic simulations will vary from run to run of the same command. The default
seed is 181.

--beta <x>
By default query-dependent banding (QDB) is used to accelerate the CM search
algorithms with a beta tail loss probability of 1E-15. This beta value can be
changed to <x> with --beta <x>. The beta parameter is the amount of probability
mass excluded during band calculation, higher values of beta give greater speedups
but sacrifice more accuracy than lower values. The default value used is 1E-15.
(For more information on QDB see Nawrocki and Eddy, PLoS Computational Biology
3(3): e56.)

--nonbanded
Turn off QDB during E-value calibration. This will slow down calibration.

--nonull3
Turn off the null3 post hoc additional null model. This is not recommended unless
you plan on using the same option to cmsearch and/or cmscan.

--random
Use the background null model of the CM to generate the random sequences, instead
of the more realistic HMM. Unless the CM was built using the --null option to
cmbuild, the background null model will be 25% each A, C, G and U.

--gc <f>
Generate the random sequences using the nucleotide distribution from the sequence
file <f>.

--cpu <n>
Specify that <n> parallel CPU workers be used. If <n> is set as "0", then the
program will be run in serial mode, without using threads. You can also control
this number by setting an environment variable, INFERNAL_NCPU. This option will
only be available if the machine on which Infernal was built is capable of using
POSIX threading (see the Installation section of the user guide for more
information).

--mpi Run as an MPI parallel program. This option will only be available if Infernal has
been configured and built with the "--enable-mpi" flag (see the Installation
section of the user guide for more information).

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