Provided by: infernal_1.1.5-2_amd64 
NAME
cmscan - search sequence(s) against a covariance model database
SYNOPSIS
cmscan [options] <cmdb> <seqfile>
DESCRIPTION
cmscan is used to search sequences against collections of covariance models. For each sequence in
<seqfile>, use that query sequence to search the target database of CMs in <cmdb>, and output ranked
lists of the CMs with the most significant matches to the sequence.
The <seqfile> may contain more than one query sequence. It can be in FASTA format, or several other
common sequence file formats (genbank, embl, and among others), or in alignment file formats (stockholm,
aligned fasta, and others). See the --qformat option for a complete list.
The <cmdb> needs to be press'ed using cmpress before it can be searched with cmscan. This creates four
binary files, suffixed .i1{fimp}. Additionally, <cmdb> must have been calibrated for E-values with
cmcalibrate before being press'ed with cmpress.
The query <seqfile> may be '-' (a dash character), in which case the query sequences are read from a
<stdin> pipe instead of from a file. The <cmdb> cannot be read from a <stdin> stream, because it needs
to have those four auxiliary binary files generated by cmpress.
The output format is designed to be human-readable, but is often so voluminous that reading it is
impractical, and parsing it is a pain. The --tblout option saves output in a simple tabular format that
is concise and easier to parse. The --fmt 2 option modifies the format of the tabular output by adding
several fields, including markup of overlapping hits, as described in section 6 of the Infernal user
guide. The -o option allows redirecting the main output, including throwing it away in /dev/null.
cmscan reexamines the 5' and 3' termini of target sequences using specialized algorithms for detection of
truncated hits, in which part of the 5' and/or 3' end of the actual full length homologous sequence is
missing in the target sequence file. These types of hits will be most common in sequence files consisting
of unassembled sequencing reads. By default, any 5' truncated hit is required to include the first
residue of the target sequence it derives from in <seqfile>, and any 3' truncated hit is required to
include the final residue of the target sequence it derives from. Any 5' and 3' truncated hit must
include the first and final residue of the target sequence it derives from. The --anytrunc option will
relax the requirements for hit inclusion of sequence endpoints, and truncated hits are allowed to start
and stop at any positions of target sequences. Importantly though, with --anytrunc, hit E-values will be
less accurate because model calibration does not consider the possibility of truncated hits, so use it
with caution. The --notrunc option can be used to turn off truncated hit detection. --notrunc will
reduce the running time of cmscan, most significantly for target <seqfile> files that include many short
sequences. Truncated hit detection is automatically turned off when the --max, --nohmm, --qdb, or
--nonbanded options are used because it relies on the use of an accelerated HMM banded alignment strategy
that is turned off by any of those options.
OPTIONS
-h Help; print a brief reminder of command line usage and all available options.
-g Turn on the glocal alignment algorithm, global with respect to the query model and local with
respect to the target database. By default, the local alignment algorithm is used which is local
with respect to both the target sequence and the model. In local mode, the alignment to span two
or more subsequences if necessary (e.g. if the structures of the query model and target sequence
are only partially shared), allowing certain large insertions and deletions in the structure to be
penalized differently than normal indels. Local mode performs better on empirical benchmarks and
is significantly more sensitive for remote homology detection. Empirically, glocal searches return
many fewer hits than local searches, so glocal may be desired for some applications.
-Z <x> Calculate E-values as if the search space size was <x> megabases (Mb). Without the use of this
option, the search space size changes for each query sequence, it is defined as the length of the
current query sequence times 2 (because both strands of the sequence will be searched) times the
number of CMs in <cmdb>.
--devhelp
Print help, as with -h , but also include expert options that are not displayed with -h . These
expert options are not expected to be relevant for the vast majority of users and so are not
described in the manual page. The only resources for understanding what they actually do are the
brief one-line descriptions output when --devhelp is enabled, and the source code.
OPTIONS FOR CONTROLLING OUTPUT
-o <f> Direct the main human-readable output to a file <f> instead of the default stdout.
--tblout <f>
Save a simple tabular (space-delimited) file summarizing the hits found, with one data line per
hit. The format of this file is described in section 6 of the Infernal user guide.
--fmt <n>
specify the format of the tabular output file specified with --tblout <f> be in format <n>.
Possible values for <n> are 1 or 2. By default <n> is 1 when --tblout is used without --fmt. With
--fmt 2 nine additional fields are added to the tabular output file, most of which pertain to the
annotation of overlapping hits. See section 6 the Infernal user guide for a description of both
formats.
--acc Use accessions instead of names in the main output, where available for profiles and/or sequences.
--noali
Omit the alignment section from the main output. This can greatly reduce the output volume.
--notextw
Unlimit the length of each line in the main output. The default is a limit of 120 characters per
line, which helps in displaying the output cleanly on terminals and in editors, but can truncate
target profile description lines.
--textw <n>
Set the main output's line length limit to <n> characters per line. The default is 120.
--verbose
Include extra search pipeline statistics in the main output, including filter survival statistics
for truncated hit detection and number of envelopes discarded due to matrix size overflows.
OPTIONS CONTROLLING REPORTING THRESHOLDS
Reporting thresholds control which hits are reported in output files (the main output and --tblout) Hits
are ranked by statistical significance (E-value). By default, all hits with an E-value <= 10 are
reported. The following options allow you to change the default E-value reporting thresholds, or to use
bit score thresholds instead.
-E <x> In the per-target output, report target sequences with an E-value of <= <x>. The default is 10.0,
meaning that on average, about 10 false positives will be reported per query, so you can see the
top of the noise and decide for yourself if it's really noise.
-T <x> Instead of thresholding per-CM output on E-value, report target sequences with a bit score of >=
<x>.
OPTIONS FOR INCLUSION THRESHOLDS
Inclusion thresholds are stricter than reporting thresholds. Inclusion thresholds control which hits are
considered to be reliable enough to be included in a possible subsequent search round, or marked as
significant ("!") as opposed to questionable ("?") in hit output.
--incE <x>
Use an E-value of <= <x> as the hit inclusion threshold. The default is 0.01, meaning that on
average, about 1 false positive would be expected in every 100 searches with different query
sequences.
--incT <x>
Instead of using E-values for setting the inclusion threshold, instead use a bit score of >= <x>
as the hit inclusion threshold. By default this option is unset.
OPTIONS FOR MODEL-SPECIFIC SCORE THRESHOLDING
Curated CM databases may define specific bit score thresholds for each CM, superseding any thresholding
based on statistical significance alone.
To use these options, the profile must contain the appropriate (GA, TC, and/or NC) optional score
threshold annotation; this is picked up by cmbuild from Stockholm format alignment files. Each
thresholding option has a score of <x> bits, and acts as if -T <x> --incT <x> has been applied
specifically using each model's curated thresholds.
--cut_ga
Use the GA (gathering) bit scores in the model to set hit reporting and inclusion thresholds. GA
thresholds are generally considered to be the reliable curated thresholds defining family
membership; for example, in Rfam, these thresholds define what gets included in Rfam Full
alignments based on searches with Rfam Seed models.
--cut_nc
Use the NC (noise cutoff) bit score thresholds in the model to set hit reporting and inclusion
thresholds. NC thresholds are generally considered to be the score of the highest-scoring known
false positive.
--cut_tc
Use the TC (trusted cutoff) bit score thresholds in the model to set hit reporting and inclusion
thresholds. TC thresholds are generally considered to be the score of the lowest-scoring known
true positive that is above all known false positives.
OPTIONS CONTROLLING THE ACCELERATION PIPELINE
Infernal searches are accelerated in a six-stage filter pipeline. The first five stages use a profile HMM
to define envelopes that are passed to the stage six CM CYK filter. Any envelopes that survive all
filters are assigned final scores using the the CM Inside algorithm.
The profile HMM filter is built by the cmbuild program and is stored in <cmfile>.
Each successive filter is slower than the previous one, but better than it at disciminating between
subsequences that may contain high-scoring CM hits and those that do not. The first three HMM filter
stages are the same as those used in HMMER3. Stage 1 (F1) is the local HMM SSV filter modified for long
sequences. Stage 2 (F2) is the local HMM Viterbi filter. Stage 3 (F3) is the local HMM Forward filter.
Each of the first three stages uses the profile HMM in local mode, which allows a target subsequence to
align to any region of the HMM. Stage 4 (F4) is a glocal HMM filter, which requires a target subsequence
to align to the full-length profile HMM. Stage 5 (F5) is the glocal HMM envelope definition filter, which
uses HMMER3's domain identification heursitics to define envelope boundaries. After each stage from 2 to
5 a bias filter step (F2b, F3b, F4b, and F5b) is used to remove sequences that appear to have passed the
filter due to biased composition alone. Any envelopes that survive stages F1 through F5b are then passed
with the local CM CYK filter. The CYK filter uses constraints (bands) derived from an HMM alignment of
the envelope to reduce the number of required calculations and save time. Any envelopes that pass CYK
are scored with the local CM Inside algorithm, again using HMM bands for acceleration.
The default filter thresholds that define the minimum score required for a subsequence to survive each
stage are defined based on the size of the search space (Z), which is defined as the length of the
current query sequence times 2 (because both strands will be searched) times the number of profiles in
<cmdb>. However, if either the -Z <x> or --FZ <x> options are used then the search space will be
considered to be <x> for purposes of defining the filter thresholds.
For larger databases, the filters are more strict leading to more acceleration but potentially a greater
loss of sensitivity. The rationale is that for larger databases, hits must have higher scores to achieve
statistical significance, so stricter filtering that removes lower scoring insignificant hits is
acceptable.
The P-value thresholds for all possible search space sizes and all filter stages are listed next. (A P-
value threshold of 0.01 means that roughly 1% of the highest scoring nonhomologous subsequence are
expected to pass the filter.) Z is defined as the number of nucleotides in the complete target sequence
file times 2 because both strands will be searched with each model.
If Z is less than 2 Mb: F1 is 0.35; F2 and F2b are off; F3, F3b, F4, F4b and F5 are 0.02; F6 is 0.0001.
If Z is between 2 Mb and 20 Mb: F1 is 0.35; F2 and F2b are off; F3, F3b, F4, F4b and F5 are 0.005; F6 is
0.0001.
If Z is between 20 Mb and 200 Mb: F1 is 0.35; F2 and F2b are 0.15; F3, F3b, F4, F4b and F5 are 0.003; F6
is 0.0001.
If Z is between 200 Mb and 2 Gb: F1 is 0.15; F2 and F2b are 0.15; F3, F3b, F4, F4b, F5, and F5b are
0.0008; and F6 is 0.0001.
If Z is between 2 Gb and 20 Gb: F1 is 0.15; F2 and F2b are 0.15; F3, F3b, F4, F4b, F5, and F5b are
0.0002; and F6 is 0.0001.
If Z is more than 20 Gb: F1 is 0.06; F2 and F2b are 0.02; F3, F3b, F4, F4b, F5, and F5b are 0.0002; and
F6 is 0.0001.
These thresholds were chosen based on performance on an internal benchmark testing many different
possible settings.
There are five options for controlling the general filtering level. These options are, in order from
least strict (slowest but most sensitive) to most strict (fastest but least sensitive): --max, --nohmm,
--mid, --default, (this is the default setting) --rfam. and --hmmonly. With --default the filter
thresholds will be database-size dependent. See the explanation of each of these individual options below
for more information.
Additionally, an expert user can precisely control each filter stage score threshold with the --F1,
--F1b, --F2, --F2b, --F3, --F3b, --F4, --F4b, --F5, --F5b, and --F6 options. As well as turn each stage
on or off with the --noF1, --doF1b, --noF2, --noF2b, --noF3, --noF3b, --noF4, --noF4b, --noF5, and
--noF6. options. These options are only displayed if the --devhelp option is used to keep the number of
displayed options with -h reasonable, and because they are only expected to be useful to a small minority
of users.
As a special case, for any models in <cmfile> which have zero basepairs, profile HMM searches are run
instead of CM searches. HMM algorithms are more efficient than CM algorithms, and the benefit of CM
algorithms is lost for models with no secondary structure (zero basepairs). These profile HMM searches
will run significantly faster than the CM searches. You can force HMM-only searches with the --hmmonly
option. For more information on HMM-only searches see the user guide.
--max Turn off all filters, and run non-banded Inside on every full-length target sequence. This
increases sensitivity somewhat, at an extremely large cost in speed.
--nohmm
Turn off all HMM filter stages (F1 through F5b). The CYK filter, using QDBs, will be run on every
full-length target sequence and will enforce a P-value threshold of 0.0001. Each subsequence that
survives CYK will be passed to Inside, which will also use QDBs (but a looser set). This increases
sensitivity somewhat, at a very large cost in speed.
--mid Turn off the HMM SSV and Viterbi filter stages (F1 through F2b). Set remaining HMM filter
thresholds (F3 through F5b) to 0.02 by default, but changeable to <x> with --Fmid <x> sequence.
This may increase sensitivity, at a significant cost in speed.
--default
Use the default filtering strategy. This option is on by default. The filter thresholds are
determined based on the database size.
--rfam Use a strict filtering strategy devised for large databases (more than 20 Gb). This will
accelerate the search at a potential cost to sensitivity.
--hmmonly
Only use the filter profile HMM for searches, do not use the CM. Only filter stages F1 through F3
will be executed, using strict P-value thresholds (0.02 for F1, 0.001 for F2 and 0.00001 for F3).
Additionally a bias composition filter is used after the F1 stage (with P=0.02 survival
threshold). Any hit that survives all stages and has an HMM E-value or bit score above the
reporting threshold will be output. The user can change the HMM-only filter thresholds and
options with --hmmF1, --hmmF2, --hmmF3, --hmmnobias, --hmmnonull2, and --hmmmax. By default,
searches for any model with zero basepairs will be run in HMM-only mode. This can be turned off,
forcing CM searches for these models with the --nohmmonly option.
--FZ <x>
Set filter thresholds as the defaults used if the database were <x> megabases (Mb). If used with
<x> greater than 20000 (20 Gb) this option has the same effect as --rfam.
--Fmid <x>
With the --mid option set the HMM filter thresholds (F3 through F5b) to <x>. By default, <x> is
0.02.
OTHER OPTIONS
--notrunc
Turn off truncated hit detection.
--anytrunc
Allow truncated hits to begin and end at any position in a target sequence. By default, 5'
truncated hits must include the first residue of their target sequence and 3' truncated hits must
include the final residue of their target sequence. With this option you may observe fewer full
length hits that extend to the beginning and end of the query CM. As of version 1.1.5, truncated
hits that end at sequence terminii with a lower score penalty than internally truncated hits are
also considered (these were not considered in 1.1x versions prior to 1.1.5). To reproduce the
behavior of this option from v1.1.4, use the --inttrunc option instead.
--nonull3
Turn off the null3 CM score corrections for biased composition. This correction is not used during
the HMM filter stages.
--mxsize <x>
Set the maximum allowable CM DP matrix size to <x> megabytes. By default this size is 128 Mb.
This should be large enough for the vast majority of searches, especially with smaller models. If
cmscan encounters an envelope in the CYK or Inside stage that requires a larger matrix, the
envelope will be discounted from consideration. This behavior is like an additional filter that
prevents expensive (slow) CM DP calculations, but at a potential cost to sensitivity. Note that
if cmscan is being run in <n> multiple threads on a multicore machine then each thread may have an
allocated matrix of up to size <x> Mb at any given time.
--smxsize <x>
Set the maximum allowable CM search DP matrix size to <x> megabytes. By default this size is 128
Mb. This option is only relevant if the CM will not use HMM banded matrices, i.e. if the --max,
--nohmm, --qdb, --fqdb, --nonbanded, or --fnonbanded options are also used. Note that if cmsearch
is being run in <n> multiple threads on a multicore machine then each thread may have an allocated
matrix of up to size <x> Mb at any given time.
--cyk Use the CYK algorithm, not Inside, to determine the final score of all hits.
--acyk Use the CYK algorithm to align hits. By default, the Durbin/Holmes optimal accuracy algorithm is
used, which finds the alignment that maximizes the expected accuracy of all aligned residues.
--wcx <x>
For each CM, set the W parameter, the expected maximum length of a hit, to <x> times the consensus
length of the model. By default, the W parameter is read from the CM file and was calculated based
on the transition probabilities of the model by cmbuild. You can find out what the default W is
for a model using cmstat. This option should be used with caution as it impacts the filtering
pipeline at several different stages in nonobvious ways. It is only recommended for expert users
searching for hits that are much longer than any of the homologs used to build the model in
cmbuild, e.g. ones with large introns or other large insertions. It cannot be used in combination
with the --nohmm, --fqdb or --qdb options because in those cases W is limited by query-dependent
bands.
--toponly
Only search the top (Watson) strand of target sequences in <seqfile>. By default, both strands
are searched. This will halve the search space size (Z).
--bottomonly
Only search the bottom (Crick) strand of target sequences in <seqfile>. By default, both strands
are searched. This will halve the search space size (Z).
--qformat <s>
Assert that the query sequence database file is in format <s>. Accepted formats include fasta,
embl, genbank, ddbj, stockholm, pfam, a2m, afa, clustal, and phylip The default is to autodetect
the format of the file.
--glist <f>
Configure a subset of models from <cmfile> in glocal alignment mode, instead of local mode, namely
the models listed in file <f>. Configure all other models (those not listed in <f>) in local
mode. This option is incompatible with -g. File <f> must list valid names of models from
<cmfile>, each separated by any whitespace character (e.g. a newline character).
--clanin <f>
Read clan information on the models in <cmfile> from file <f>. Not all models in <cmfile> need to
be a member of a clan. This option must be used in combination with --fmt 2 and --tblout because
clan annotation is only output in format 2 of the tabular output file. See section 9 of the
Infernal user guide for specifications on the format of the clan input file <f>.
--oclan
Only mark overlaps between models in the same clan. This option must be used in combination with
--fmt 2 , --tblout and --clanin because clan annotation is only output in format 2 of the tabular
output file, and clan information can only be input using the --clanin option.
--oskip
Omit any hit h from the tabular output file that satisfies the following: another hit h2 overlaps
with h and the E-value of h2 is lower than that of h, and h2 is itself not omitted. Hit h will not
appear in the tabular output file, although it will still exist in the standard output. This
option must be used in combination with --fmt 2 --tblout because overlap annotation is only output
in format 2 of the tabular output file. When used in combination with --oclan only hits h that
satisfy the following are omitted: another hit h2 overlaps with h, the E-value of h2 is lower than
that of h, and both h and h2 are hits to models that are in the same clan.
--cpu <n>
Set the number of parallel worker threads to <n>. On multicore machines, the default is 4. You
can also control this number by setting an environment variable, INFERNAL_NCPU. There is also a
master thread, so the actual number of threads that Infernal spawns is <n>+1. This option is not
available if Infernal was compiled with POSIX threads support turned off.
--stall
For debugging the MPI master/worker version: pause after start, to enable the developer to attach
debuggers to the running master and worker(s) processes. Send SIGCONT signal to release the pause.
(Under gdb: (gdb) signal SIGCONT) (Only available if optional MPI support was enabled at compile-
time.)
--mpi Run in MPI master/worker mode, using mpirun. (Only available if optional MPI support was enabled
at compile-time.)
SEE ALSO
See infernal(1) for a master man page with a list of all the individual man pages for programs in the
Infernal package.
For complete documentation, see the user guide that came with your Infernal distribution (Userguide.pdf);
or see the Infernal web page (http://eddylab.org/infernal/).
COPYRIGHT
Copyright (C) 2023 Howard Hughes Medical Institute.
Freely distributed under the BSD open source license.
For additional information on copyright and licensing, see the file called COPYRIGHT in your Infernal
source distribution, or see the Infernal web page (http://eddylab.org/infernal/).
AUTHOR
http://eddylab.org
Infernal 1.1.5 Sep 2023 cmscan(1)