1hmmpgmd(1)                       HMMER Manual                       hmmpgmd(1)
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NAME

6       hmmpgmd - daemon for database search web services
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SYNOPSIS

11       hmmpgmd [options]
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DESCRIPTION

16       The  hmmpgmd  program  is the daemon that we use internally for the hm‐
17       mer.org web server.  It essentially stands in front of the search  pro‐
18       grams phmmer, hmmsearch, and hmmscan.
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21       To  use  hmmpgmd,  first  an  instance  must  be started up as a master
22       server, and provided with at least one  sequence  database  (using  the
23       --seqdb  flag)  and/or an HMM database (using the --hmmdb flag).  A se‐
24       quence database must be in hmmpgmd format, which may be produced  using
25       esl-reformat.   An  HMM  database  is of the form produced by hmmbuild.
26       The input database(s) will be loaded into memory by  the  master.  When
27       the  master  has  finished loading the database(s), it prints the line:
28       "Data loaded into memory. Master is ready."
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32       After the master is ready, one or more  instances  of  hmmpgmd  may  be
33       started as workers. These workers may be (and typically are) on differ‐
34       ent machines from the master, but must have access to the same database
35       file(s) provided to the master, with the same path. As with the master,
36       each worker loads the database(s) into memory, and indicates completion
37       by printing: "Data loaded into memory. Worker is ready."
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41       The  master process and workers are expected to remain running.  One or
42       more clients then connect  to  the  master  and  submit  possibly  many
43       queries.  The master distributes the work of a query among the workers,
44       collects results, and merges them before responding to the client.  Two
45       example client programs are included in the HMMER src directory - the C
46       program hmmc2 and the perl script hmmpgmd_client_example.pl.  These are
47       intended  as examples only, and should be extended as necessary to meet
48       your needs.
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51       A query is submitted to the master  from  the  client  as  a  character
52       string.  Queries may be the sort that would normally be handled by phm‐
53       mer (protein sequence vs  protein  database),  hmmsearch  (protein  HMM
54       query  vs  protein  database), or hmmscan (protein query vs protein HMM
55       database).
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58       The general form of a client query is to start with a  single  line  of
59       the  form  @[options],  followed by multiple lines of text representing
60       either the query HMM or fasta-formatted sequence.  The  final  line  of
61       each query is the separator //.
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65       For  example,  to  perform a phmmer type search of a sequence against a
66       sequence database file, the first line is of the form @--seqdb 1,  then
67       the  fasta-formatted  query sequence starting with the header line >se‐
68       quence-name, followed by one or more lines of sequence, and finally the
69       closing //.
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72       To  perform an hmmsearch type search, the query sequence is replaced by
73       the full text of a HMMER-format query HMM.
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76       To perform an hmmscan type search, the text matches that of the  phmmer
77       type search, except that the first line changes to @--hmmdb 1.
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80       In  the  hmmpgmd-formatted sequence database file, each sequence can be
81       associated with one or more sub-databases. The --seqdb  flag  indicates
82       which  of these sub-databases will be queried.  The HMM database format
83       does not support sub-databases.
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OPTIONS

90       -h     Help; print a brief reminder  of  command  line  usage  and  all
91              available options.
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94       --master
95              Run as the master server.
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98       --worker <s>
99              Run as a worker, connecting to the master server that is running
100              on IP address <s>.
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103       --cport <n>
104              Port to use for communication between  clients  and  the  master
105              server.  The default is 51371.
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108       --wport <n>
109              Port  to  use  for  communication between workers and the master
110              server.  The default is 51372.
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113       --ccncts <n>
114              Maximum number of client connections to accept. The  default  is
115              16.
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118       --wcncts <n>
119              Maximum  number  of worker connections to accept. The default is
120              32.
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123       --pid <f>
124              Name of file into which the process id will be written.
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127       --seqdb <f>
128              Name of the file (in  hmmpgmd  format)  containing  protein  se‐
129              quences.  The contents of this file will be cached for searches.
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132       --hmmdb <f>
133              Name  of  the file containing protein HMMs. The contents of this
134              file will be cached for searches.
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137       --cpu <n>
138              Number of parallel threads to use (for --worker ).
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SEE ALSO

143       See hmmer(1) for a master man page with a list of  all  the  individual
144       man pages for programs in the HMMER package.
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147       For  complete documentation, see the user guide that came with your HM‐
148       MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
149       mer.org/).
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155       Copyright (C) 2020 Howard Hughes Medical Institute.
156       Freely distributed under the BSD open source license.
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158       For  additional  information  on  copyright and licensing, see the file
159       called COPYRIGHT in your HMMER source distribution, or  see  the  HMMER
160       web page (http://hmmer.org/).
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AUTHOR

165       http://eddylab.org
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172HMMER 3.3.2                        Nov 2020                         hmmpgmd(1)
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