Installation of RECOG local server - PukiWiki

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Installation of RECOG local server
Building data on RECOG local server
Supported OS
Requirements
Download
User setting
File extraction
Setup the RECOG server
Automatic setup by Configure script
Setup the RECOG server manually (skip if Configure is successfully finished)
MySQL setup
Tips on MySQL server
Utility commands for MySQL server
Setting up Apache httpd serverStarting the httpd server
Stopping the httpd server

Supported OS †Linux (currently tested on CentOS5 [http://www.centos.org/] )Mac OS X (10.4 or later, Intel)!

Requirements†

The following external programs are needed to be installed on your computer before you install the RECOG
system.
Software Mandatory

Explanation

Remarks

Perl

Yes

Scripting language

Version 5.8 or more

GCC

Yes

Compiling C programs

MySQL

Yes

Database management system

Version 5.0 or more

ApacheYes

HTTP server

Version 2.0 or more

Curl

Yes

File transfer

BLAST

Yes

Similarity search

ClustalW

No

Constructing multiple alignments

MAFFT

No

Constructing multiple alignments

PHYLIP

No

Constructing phylogenetic trees

GD LibraryNo

Drawing comparative genome maps

Version 2.0 or more!

Download†

The latest version of RECOG is available at:
http://bias.nibb.ac.jp/RECOG/
Downloaded file is recog-server-x.y.z.tar.gz, where x.y.z is a version number.
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User setting †We recommend you to create a specific UNIX user account for administrating the RECOG system becausesome setting required for RECOG administration (e.g. MySQL setting) might conflict with your own setting. In
the following, we assume the following administrator user account.
Item

Value

User namerecogadm

Group name recog

All of the administrative operations below should be done by this user.
!

File extraction†

In the following, we assume you will install the recog server on the user's home directory ($HOME) anddownloaded file is saved in /tmp directory.
% cd $HOME% tar xfz /tmp/recog-server-x.y.z.tar.gz

A new directory named RECOG-server is created. Hereafter, we call this directory RECOG_HOME.
!

Setup the RECOG server †!

Automatic setup by Configure script†

There is a script named Configure in the $RECOG_HOME directory that executes all required setup. First, youare asked to set several parameters required for setting up the server.
Parameter

Explanation

RECOG home

Name of RECOG_HOME directory (= current directory)

Blast path

Path of the blastall program

Mysql basedir

Prefix directory for MySQL directories including binary (bin), library (lib) etc.

Mysql datadir

Directory storing MySQL data for RECOG system

Apache httpd.conf file Path of httpd.conf file
Server address

IP address of the server

Server httpd port

Port number for server httpd

Qstat path

Path for qstat command

Working dir for qsub

Working directory for qsub that should be accessible for all cluster nodes

Queue name

Queue name for qsub (with -q option)

Typically an appropriate value should be proposed in square brackets, so you can just type return key if you
accept this default value, but you can modify it if required.
Example session:% cd $RECOG_HOME% ./Configure
RECOG home [/home/recogadm/project/proj1/RECOG-server]:https://bias.nibb.ac.jp:8039/pukiwiki/?Installation%20of%20RECOG%20local%20server

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RECOG home [/home/recogadm/project/proj1/RECOG-server]:RECOG_HOME=/home/recogadm/project/proj1/RECOG-server
Blast path [/usr/local/bin/blastall]:
Mysql basedir [/usr/local/mysql]:
Mysql datadir [/home/recogadm/project/proj1/RECOG-server/mysql]:
Apache httpd.conf file [/etc/httpd/conf/httpd.conf]:
Server address [123.45.67.89]:
Server httpd port [8080]:
Do you use queuing system (y/n)? [y]:Qstat path [/opt/gridengine/bin/lx24-amd64/qstat]:Working dir for qsub [/home/recogadm/project/proj1/RECOG-server/work/qsub]:Queue name [<default queue>]:

If the Configure script is successfully finished, you can skip most of the following procedures; just you should
go to "Access control" (the last subsection in the "Setting up Apache httpd server" section) and modify access
control, then start the httpd server to finish the server setup.
If the script does not work, you should check individual steps that do not work correctly. See the following
section and try manual setup explained there.
!

Setup the RECOG server manually (skip if Configure is successfully finished)†

We assume RECOG_HOME is $HOME/RECOG-server and operations are done by the user "recogadm".
1. Setting environmental variables
sh/bash% export RECOG_HOME=$HOME/RECOG-server% export PERLLIB=$RECOG_HOME/perllib

csh/tcsh% setenv RECOG_HOME $HOME/RECOG-server% setenv PERLLIB $RECOG_HOME/perllib

2. Execute the configure script
For a single node server (without any queueing system)
Execute the configure script as follows% cd $RECOG_HOME/perllib% autoconf% ./configure ¥> --with-recogadm-passwd=recogadm_password ¥> --with-blast-dir=/usr/local/blast ¥> --with-mysql-dir=/usr/local/mysql

If the configure does not detect some commands, use the following options
OptionExplanation--with-recogadm-passwd The password of the administrator（recogadm）in the web interface.
--with-blast-dir

The path for the BLAST commands--with-clustalw-dir

The path for the clustalw command--with-mafft-dir

The path for the mafft command--with-imagemagick-dir

The path for the ImageMagick commands--with-mysql-dir

The path for the MySQL commands--with-curl-dir

The path for the curl command

For a multiple node cluster with a Network Queuing System (currently RECOG supports Sun Grid
Engine only):https://bias.nibb.ac.jp:8039/pukiwiki/?Installation%20of%20RECOG%20local%20server

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% cd $RECOG_HOME/perllib% autoconf% ./configure ¥> --with-recogadm-passwd=recogadm_password ¥> --with-blast-dir=/usr/local/blast ¥> --with-mysql-dir=/usr/local/mysql ¥> --with-nqs-dir=/usr/local/sge/OS ¥> --with-nqs-pub-dir=/home/USER/local/pub_nqs ¥> --with-nqs-max-nodes=3 ¥> --with-nqs-queue=queue_name

If the configure does not detect some NQS specific commands, use the following options
OptionExplanation--with-nqs-dir

Directory for qsub/qstat commands--with-nqs-queue

Queue name for submitting jobs to the NQS system
Default: default queue set in the NQS system--with-nqs-pub-dir

Directory shared among NQS nodes
Results are stored in a directory named UserName under this directory.

--with-nqs-max-nodes

The maximum number of nodes used for submitting NQS sjobs--with-sge-root

Set the environmental variable SGE_ROOT used in Sun Grid Engine--with-sge-cell

Set the environmental variable SGE_CELL used in Sun Grid Engine--with-sge-clustername

Set the environmental variable SGE_CLUSTER_NAME used in Sun Grid
Engine--with-sge-execd-port

Set the environmental variable SGE_EXECD_PORT used in Sun Grid Engine--with-sge-qmasterport

Set the environmental variable SGE_QMASTER_PORT used in Sun Grid
Engine3. Setup file for environmental variables
Environment setup files are generated in the $RECOG_HOME/etc directory, which can be used to set theenvironmental variables required for the administrator's tasks. Read the files as follows before any
administrative operation described below.
For sh/bash% . $RECOG_HOME/etc/recog.sh

For csh/tcsh% source $RECOG_HOME/etc/recog.csh!

MySQL setup†

Each RECOG server uses an independent MySQL server, so you need to set up a MySQL server even if yoursystem already have one. The following procedures set up MySQL database for the RECOG server.
1. Configuring MySQL
Move to the $RECOG_HOME/build/mysql directory and execute configure command. This command setup
a new MySQL server including the setup of MySQL users and generating database. You must determine
and remember the root password, name and password of mysql user for storing RECOG database.
OptionExplanation--with-base-dir

Path for the MySQL server commands--with-data-dir

Path for storing the MySQL database--with-root-passwd

Password for the MySQL administrator (=root)

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MySQL user account name used by RECOG server--with-user-passwd Password for the RECOG user

Example% cd $RECOG_HOME/build/mysql% autoconf% ./configure ¥> --with-base-dir=/usr/local/mysql ¥> --with-data-dir=$RECOG_HOME/mysql ¥> --with-root-passwd=root_password ¥> --with-user-name=recog ¥> --with-user-passwd=password

2. Testing MySQL server
Execute the following command to check whether mysql server can be started correctly% /usr/local/mysql/bin/mysql --defaults-file=$RECOG_HOME/etc/my.cnf -e 'show status'

If it has successfully started up, then the following information is displayed.
+-----------------------------------+----------+| Variable_name| Value|+-----------------------------------+----------+| Aborted_clients| 0|(snip)| Uptime_since_flush_status| 23|+-----------------------------------+----------+

The following message is displayed if the MySQL server is failed to start.
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/mysql/mysql.sock' (2)!

Tips on MySQL server †We assume the server machine on which MySQL server runs has at least 2GB of memory.
If your machine has larger memory size, increasing the following parameter by modifying$RECOG_HOME/etc/my.cnf can enhance the performance.
key_buffer_size
The value is in default 512M. The following example increases it to 2GB.
key_buffer_size=2G!

Utility commands for MySQL server †The following commands can be used to manage the MySQL server.
Starting and stopping MySQL serverStart the MySQL server
The following command start the mysql server. This should be done whenever you reboot the servermachine.
% cd $RECOG_HOME/bin% ./startup_mysql.sh

Stop the MySQL server
The following command stop the mysql server. This should be done when you shutdown the servermachine.
You need to enter the MySQL administrator's password
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You need to enter the MySQL administrator's password% cd $RECOG_HOME/bin% ./shutdown_mysql.shInitializing the MySQL database [#a0def30a] The following command can be used to re-initialize the
MySQL database.
[NOTE] This command delete all data and you cannot recover them.
% cd $RECOG_HOME/build/mysql% ./create_recog_databases.sh!

Setting up Apache httpd server†

RECOG server also uses an independent httpd server. Execute the following to configure the server.
1. Copying httpd.conf file
Copy the system standard httpd.conf file into the RECOG system. The location of the standard httpd.conf
file may be different between systems. For example, /etc/httpd/conf/httpd.conf in Red Hat EnterpriseLinux and /etc/apache2/httpd.conf in MacOS 10.6. After copying it, you should add a line indicating toinclude the RECOG specific configuration as follows:
For Red Hat Linux (CentOS) (change the location of httpd.conf file for your system)% cd $RECOG_HOME/WWW/conf% cp /etc/httpd/conf/httpd.conf .
% echo "Include $RECOG_HOME/WWW/conf/httpd-recog.conf" >> httpd.conf

2. Edit the configuration file $RECOG_HOME/WWW/conf/httpd.conf
Modify the copied httpd.conf file to make the description in httpd-recog.conf effective.
i. Modify the address and the port number of the httpd server.
Before#Listen 12.34.56.78:80
Listen 80

After#Listen 12.34.56.78:80
Listen 192.168.123.45:8080(192.168.123.45 is an example of IP address. Replace it with the address of your own machine.
Also, 808 is the default port number in the RECOG system, but you can modify it if this number
has already been used by other service)
ii. Nullify the CustomLog directive (location of the httpd log files), which activate the location describedin httpd-recog.conf file.
BeforeCustomLog logs/access_log common

The location might be different. For example, it might be
CustomLog /private/var/log/apache2/access_log common

After（Comment out by adding '#'）
#CustomLog logs/access_log common

iii. Comment out the directive to load mod_ssl module.
BeforeLoadModule ssl_module libexec/apache2/mod_ssl.so
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After（Comment out by adding '#'）
#LoadModule ssl_module libexec/apache2/mod_ssl.so

3. Access control [REQUIRED]For security reason, all connections are disabled in the initial setting. So you MUST modify it to enable
connection at least from your machine on which you will execute the RECOG client
Initially, the access control is described in $RECOG_HOME/WWW/conf/httpd-recog.conf as follows:#

Order deny,allow
Deny from all
Allow from host.example.com

If you intend to allow access from any site, edit $RECOG_HOME/WWW/conf/httpd-recog.conf as
follows (comment out the Deny directive):##

Deny from all
Allow from host.example.com

If you intend to allow access from limited sites, edit $RECOG_HOME/WWW/conf/httpd-recog.conf to
add the IP addresses or the host/domain names of the allowed sites
Order deny,allow
Deny from all
Allow from host.example.com
Allow from .example.com
Allow from 192.168.1.23
Allow from 192.168.2.0/24!

Starting the httpd server †1. Starting the httpd server
Execute the following command to invoke the httpd server. Note that the command path of httpd might
be different in your system.
% /usr/sbin/httpd -f $RECOG_HOME/WWW/conf/httpd.conf

2. Checking the invocation of the httpd server
Access the following URL on your web browser
http://(server IP address):8080/index.html(The port number 8080 should also be modified if you set the other port number)
The server works well if the browser displays 'RECOG-server'.
!

Stopping the httpd server†

1. Stopping the httpd server
Execute the following command to stop the httpd server.
% kill `cat $RECOG_HOME/WWW/logs/httpd.pid`

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Building data on RECOG local server
Installation of RECOG local server

Building data on RECOG local server †Building data on RECOG local server
Data update (command line interface)!

Data update (command line interface) †1. Setup environmental variables
Set environmental variables by reading the setup file. Note that $RECOG_HOME is the top
directory of RECOG server.
For sh/bash% . $RECOG_HOME/etc/recog.sh

For csh/tcsh% source $RECOG_HOME/etc/recog.csh

2. Update taxonomy database
Download and update the taxonomy database from the following NCBI site
ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz% cd $RECOG_HOME/build% ./m0110convTaxonomyDb.pl

3. Update CDD database
Download and update the CDD database from the following NCBI site
ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cdd.tar.gz% cd $RECOG_HOME/build% ./m0020cddDb.pl

4. Update additional databases
Download and update additional databases from the following sites
KEGG: http://www.genome.jp/kegg/catalog/org_list.html
NCBI Genomes: http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi?dump=selected
GOLD: http://www.genomesonline.org/DBs/gold_published_table.txt% cd $RECOG_HOME/build% ./m0050kegg.pl% ./m0051ncbi.pl% ./m0052gold.pl

5. Update motif identifier table
Download and update the motif identifier table from NCBI
ftp://ftp.ncbi.nih.gov/pub/mmdb/cdd/cddid.tbl.gz
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% cd $RECOG_HOME/build% ./m0120motifTab.pl -DOWNLOAD

6. Download published genome data from the MBGD server
Download and update specified published genome data. To find the genome identifiers (gmnumbers) see the following URL
http://mbgd.genome.ad.jp/data/species/spid.tab% cd $RECOG_HOME/build% ./mirrorSpidData.pl gm00001 gm00002 gm00003 gm00004 gm00005

7. Input user genome data
Skip here if you need not add or update your original genome data.
See [ Preparation of user genome data ] to prepare and input the user genome data.
8. Check $RECOG_HOME/etc/spid.tab file Check the list of target species
The following information is listed for each genome with the tab-delimited format.
i. spid : species ID
The public RECOG data is numbered in 'gm99999' format
User genome data is numbered in 'gu99999' format
ii. spname : species code
The species code in 3-5 lettersiii. dir-name : FTP directoryThis field is used only for published data. For user genome data, species name is filledhere【例】
http://mbgd.genome.ad.jp/data/species/spid.tab
9. Insert species data into the MySQL databae
Insert species data
% ./m0400InsertSpecInfo.pl

Remove checkpoint files
After execution, checkpoint file is created. Remove the corresponding checkpoint files if
you want to re-execute some failed procedure.
% /bin/rm -f $RECOG_HOME/work/.m04*

Check inserted data
check all genome data
% ./viewUserGenomeData.pl -ALL

Check only specified species (with species ID)% ./viewUserGenomeData.pl gu00001

Remove data from the MySQL database
Remove all data of specified genome from the MySQL database when there are somemistake. [NOTE] You cannot recover deleted data.
Remove data with species ID% ./removeUserGenomeData.pl gu01234

10. Definition of species set
By default, all-against-all comparison will be done among all the defined genome sequences,
but you can limit calculation by defining "species sets": if a species set is defined, RECOG
calculates all-against-all similarity only among the defined species sets.
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Editing the species set file% vi $RECOG_HOME/etc/spid_set/spid_set.tab

Format
The following items are listed in the tab-delimited format.
Name

Explanation

name

Name of species set

species list

List of spid or species_code
multiple species should be separated by a comma

11. Execute homology search
Execute homology search% ./m0500ExecSearch.pl

Remove check point file
Remove the corresponding checkpoint files if you want to re-execute some failed
procedure.
% /bin/rm -f $RECOG_HOME/work/.m05*

12. Insert homology search result into the MySQL database
Insert data into the database% ./m1000InsertSearchRes.pl

Remove checkpoint file
Remove the corresponding checkpoint files if you want to re-execute some failed
procedure.
% /bin/rm -f $RECOG_HOME/work/.m10*

13. Expand homology search result
Execute expansion and additional post-processing% ./m1100BuildData.pl -all

If you need to re-execute 1120CopyHomologyInfo.pl in the middle of the execution, youmust remove the following files.
% /bin/rm -f $RECOG_HOME/work/homologyMd5.$PID% /bin/rm -f $RECOG_HOME/work/homologySp.$PID

Remove checkpoint file
Remove the corresponding checkpoint files if you want to re-execute some failed
procedure.
% /bin/rm -f $RECOG_HOME/work/.m11*% /bin/rm -f $RECOG_HOME/work/homologyMd5.INPUT% /bin/rm -f $RECOG_HOME/work/homologySp.INPUT

14. Publishing the database% ./m1200PublishInfo.pl

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Preparation of user genome data
Building data on RECOG local server

Preparation of user genome data †Your data should be prepared in GenBank format or a combination of FASTA sequence files and tabdelimited annotation files.
!

GenBank format files†

If your data is already in GenBank format, what you should do is minimum.
1. Determine the species code of your genome
Determine the species code of your genome based on the following rules:
i. The length of species code is between 3 and 5.
ii. The first letter should be a lower alphabetical character.
iii. The other letters should be lower alphabetical or numeric characters.
iv. The code should not be used yet for other species in the database.
Species codes of the published genomes are basically same as that of the KEGG database,which are found in http://mbgd.genome.ad.jp/data/species/spid.tab( e.g., the species code of Haemophilus_influenzae is hin)
2. Generate a data directory and template files
Execute the following command to create a data directory and template data files
In addition to the above species code, you need to specify the number ofchromosomes/plasmid (using -nchr option).
% cd $RECOG_HOME/build% ./createUgSkeleton.pl -sp=species_code -nchr=num_chromosomes
Create skeleton for guXXXXX

where guXXXXX is an automatically generated species identifier (XXXXX is a serial number). In
this case, a data directory is $RECOG_HOME/species/guXXXXX and template files are createdthere.
3. Put your data in the created directory
Put your data in the "GB" directory in the created directory($RECOG_HOME/species/guXXXXX/GB). Create directory manually if there exists no suchdirecgtory.
Name each file as 1.gbk, 2.gbk, ... according to the chromosome numbers (or your desiredorder of chromosomes).
% cd $RECOG_HOME/species/guXXXXX% mkdir GB

4. Conversion the GenBank file
Execute the following command to extract data from the GenBank files.
% cd $RECOG_HOME/build% ./m0310ConvGB2Mbgd.pl

guXXXXX

Add -contig option when processing incomplete genome data.
% ./m0310ConvGB2Mbgd.pl-contig

guXXXXX

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Add also -NO_LOCATION option if you need not extract location information (beginning andending positions on the chromosome sequence) of each gene.This is especially useful for
metagenomic data.
% ./m0310ConvGB2Mbgd.pl-contig-NO_LOCATION

guXXXXX!

FASTA sequence files and Tab-delimited text files†

You can also put the information with a combination of FASTA sequence files and tab-delimited text
files. To do this, you should prepare the following:
1. Generate a data directory and template files
Determine the species code of your genomes referring to the above "GenBank format files"
section. Also, count the number of chromosomes/plasmids.
Execute the following command to create a data directory and template data files% cd $RECOG_HOME/build% ./createUgSkeleton.pl -sp=species_code
Create skeleton for guXXXXX-nchr=num_chromosomes

where guXXXXX is an automatically generated species identifier and a data directory named$RECOG_HOME/species/guXXXXX is created.
2. Edit genome data
Edit the file $RECOG_HOME/species/guXXXXX/gm/genome.txt to put genomic information. The
file should include the following information:
Name

Mandatory

Explanation

Remarkssp

Yes

species codee.g.) 'hin'abbrev

Yes

Abbreviated species namee.g.) 'H.influenzae'orgnameYes

Full species namee.g.) 'Haemophilus influenzae'strainYes

Strain namee.g.) 'Rd KW20'

taxid

Yes

taxonomy IDe.g.) '71421'

type

No

genome typecomplete / incomplete / metagenome
default: complete

date_release Yes

Release date (year-monthdate)e.g.) 1995-07-28'

specweight

Weight of species

default: (20300000−
published_date)*100

No

An example of genome data:
sp <TAB> hinabbrev <TAB> H.influenzaeorgname <TAB> Haemophilus influenzae
strain <TAB> Rd KW20
taxid <TAB> 71421
date_release<TAB> 1995-07-28
specweight <TAB>

3. Putting data for each chromosome/gene information
Put your chromosome/gene data according to the following directions.
You should specify at least gene information and protein sequences. Other information can behttps://bias.nibb.ac.jp:8039/pukiwiki/?Preparation%20of%20user%20genome%20data

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omitted if no chromosome/contig map information is available.
In the following, $(ChrNo) should be replaced with a serial number of chromosome (1,2,3,...).
i. Chromosome (or contig) information (optional)
Edit the file $RECOG_HOME/species/guXXXXX/gm/data/$(ChrNo).chromosome.txt.
Name Mandatory

Explanation

Remarks

name

Yes

Chromosome namee.g.) 'chromosome 1'

shape

Yes

Shape of chromosome 'circular' or 'linear'

type

Yes

Type

'chromosome' , 'plasmid', or 'contig'

lengthNo*

Lengthe.g.) '1830138'(*) Omissible if you specify a chromosomal sequence file (DNAseq).
An example of chromosome data:name <TAB> chromosome 1
shape <TAB> circular
type <TAB> chromosome
length <TAB> 1830138

ii. Gene information (mandatory)
For each chromosome, put gene data in that chromosome as a file named$RECOG_HOME/species/guXXXXX/gm/data/'$(ChrNo).gene, where each line contains agene information consisting the following items, which are described as a tab-delimited
format.
Name

Mandatory

Explanation

Remarks

Gene_ID Yes

Gene Identifier

Gene
name

No

Gene name

No

Start positionon thechromosome
sequenceNo

End position onthechromosome
sequence

Start < End

Direction Yes

Direction

1/-1
Specify 1 if you omit Start/End positions

type

Yes

Type of gene

CDS/misc_RNA/rRNA/tRNA/scRNA/snRNA/snoRNA/...

Product
name

No

Name ofproduct

Start
positionEnd
positionMust be unique in the genome. e.g.) locus tagiii. Protein sequence (mandatory)
Put protein sequence data as a FASTA-formatted file named$RECOG_HOME/species/guXXXXX/gm/data/$(ChrNo).protseq.
Entry name of the sequence should correspond to the gene identifier (Gene_ID) in thegene information file described above.
>Gene_ID
MAIKIGINGFGRIGRIVFRAAQHRDDIEVVGINDLIDVEYMAYMLKYDSTHGRFDGTVEVKDGNLVVNGKTIRVTAERDPANLNWGAIGVDIAVEATGLFLTDETARKHITAGAKKVVLTGPSKDATPMFVRGVNFNAYAGQDIVSNASCTTNCLAPLARVVHETFGIKDGLMTTVHATT
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ATQKTVDGPSAKDWRGGRGASQNIIPSSTGAAKAVGKVLPALNGKLTGMAFRVPTPNVSVVDLTVNLEKPASYDAIKQAIKDAAEGKTFNGELKGVLGYTEDAVVSTDFNGCALTSVFDADAGIALTDSFVKLVSWYDNETGYSNKVLDLVAHIYNYKG

iv. Chromosomal DNA sequence (DNA seq) (optional)
Put chromosomal sequence data as a file named$RECOG_HOME/species/guXXXXX/gm/data/$(ChrNo).chrseq.
v. Gene DNA sequence (optional)
If you already have gene sequence information,
put the sequence data as a FASTA-formatted file named$RECOG_HOME/species/guXXXXX/gm/data/$(ChrNo).geneseq.
If you do not have gene sequence information, but have chromosome sequences,
execute the following command to generate gene sequences using Start/End column
in the gene information file.
% cd $RECOG_HOME/build% ./convertDna2GeneSeq.pl guXXXXX

If you have neither gene sequences nor chromosomal DNA sequences,
do nothing and skip registering gene sequences.
4. Checking the data
The following command checks whether the data you input is defined correctly.
Correct data if you encounter some errors.
% cd $RECOG_HOME_build% ./checkUserGenomeData.pl -spid=guXXXXX

The following problems are reported as 'Error'.
a. In genome.txt, one of sp/orgname/taxid/release field is null.
b. In genome.txt, the specified species_code has already been used in$RECOG_HOME/etc/spid.tab.
c. In genome.txt, Illegal date_release.
d. In chromosome.txt, shape value is nether 'circular' nor 'linear'.
e. In chromosome.txt, type is neither 'chromosome', 'plasmid', nor 'contig'.
f. In chromosome.txt , both length and chrseq is empty.
g. In gene information, some mandatory items (Gene_ID, dir) are null.
h. In gene information, only one of the boundary positions (Start/End) is specified.
i. In gene information, Gene_ID is not uniquely defined.
j. No protein seq file exists for some genes.
The following possible problems are also reported as 'Warning'; some of them will be
automatically fixed by the program when you specify -UPDATE option (see below).
a. In genome.txt, abbrev field is empty. Generate based on orgname defined ingenome.txt .
b. In genome.txt, specified taxid cannot be found in the Taxonomy database. Set taxid
as 32644 (unknown).
c. No chromosome/chrseq file corresponding to some genes.
d. In chromosome.txt, length field is null. Automatically generate from the DNA seq
data.
e. In gene information, boundary position does not satisfy the required condition Start< End. In such a case, two positions are automatically exchanged.
However, if it satisfies (chromosome length / 2) < abs(End - Start), RECOG considers
that the gene spans the origin of a circular genome and does not exchange thepositions.
f. Protein or DNA sequences contain non-alphabetical characters. Such characters areautomatically removed.
5. Automatic problem fix
After having solved the detected problems, execute the following command to fix the problems
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After having solved the detected problems, execute the following command to fix the problems
reported in the Warning messages. If you encounter errors again, fix them manually and reexecute the command.
% cd $RECOG_HOME_build% ./checkUserGenomeData.pl -spid=guXXXXX -UPDATE

Last-modified: 2010-12-24 (金) 10:47:01 (770d)
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