Manatee 2.10.1 Beta Problems - MLDBM error

2010-01-25
2013-01-28
  • Greg Harhay

    Greg Harhay - 2010-01-25

    I recently installed manatee 2.10.1 beta on my Ubuntu 9.10 server (32-bit)  with MySQL. Running scripts involving the db files in the  …/lookup_files directory fail  with manatee errors such as:

    Can't tie lookup file - /usr/local/share/new_apps/manatee/lookup_files/role_data.db: at Manatee/ChadoManateeDB.pm line 4070.

    The apache2 error.log for this event is:

        ann_tools.cgi: MLDBM error: Second level tie failed, "" at Manatee/ChadoManateeDB.pm line 4070, referer: http://harhay/tigr-scripts/chado_prok_manatee/gen_sum.cgi?db=cgsp
        ann_tools.cgi: Can't tie lookup file - /usr/local/share/new_apps/manatee/lookup_files/role_data.db:  at Manatee/ChadoManateeDB.pm line 4070., referer: http://harhay/tigr-scripts/chado_prok_manatee/gen_sum.cgi?db=cgsp


    It appears that  manatee isn't correctly reading the files in the lookup_files directory causing the following error:


    MLDBM error: Second level tie failed, "" .

    Is it possible that my versions of perl  /  MLDBM   are incompatible with these db files?  Could you suggest a solution?

     
  • Todd Creasy

    Todd Creasy - 2010-02-09

    I would check 2 things.  (1) Make sure that role_data.db exists.  If it does, (2) make sure the permissions are open.  If this doesn't work, we'll have to look into other problems that might be occurring.  The lookup files are platform specific but we built them on Linux so that "shouldn't" be a problem.  Let me know how the 2 issues above work out and we'll move on from there.

    todd

     
  • James Lowey

    James Lowey - 2010-02-26

    I Actually ran into this issue when installing new beta, noticed that for some reason the role_data.db file was a tar file, (without the .tar extension)  I untarred it and it works now.

    However I am now having another problem that is similar,

    This is the error - Can't tie lookup file - : No such file or directory at ../shared/Coati/Coati/ChadoCoatiDB.pm line 13660.

    Here are the log files from apache -
    10.55.149.34 - -  "POST /tigr-scripts/chado_prok_manatee/submit_begin_all.cgi HTTP/1.1" 200 187192 "http://10.48.2.49/tigr-scripts/chado_prok_manatee/ann_tools.cgi?db=cgsp" "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.1.8) Gecko/20100202 Firefox/3.5.8 (.NET CLR 3.5.30729)"
    10.55.149.34 - -  "GET /tigr-scripts/chado_prok_manatee/shared/ORF_infopage.cgi?db=cgsp&orf=cgsp.transcript.141922013.1 HTTP/1.1" 200 1279 "http://10.48.2.49/tigr-scripts/chado_prok_manatee/submit_begin_all.cgi" "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-US; rv:1.9.1.8) Gecko/20100202 Firefox/3.5.8 (.NET CLR 3.5.30729)"

    I can provide mysql log files as well if that would be helpful

    I also noted that there are two role_data files in the installation directory :
    ~/linux_manatee_install_beta/install_chado_databases/lookup_files# ls -l
    total 2492
    -rwxrwxrwx 1 1062 kjohnson 1044377 2009-04-30 12:11 coding_hmm.lib.db.gz
    -rwxrwxrwx 1 1062 kjohnson  127118 2009-07-14 07:56 ec2go.db.gz
    -rwxrwxrwx 1 1062 kjohnson  117832 2009-07-14 07:55 hmm_go.db.gz
    -rwxrwxrwx 1 1062 kjohnson   90917 2009-07-14 07:56 prosite.db.gz
    -rwxrwxrwx 1 1062 kjohnson   86016 2009-07-14 07:56 role_data.db
    -rwxrwxrwx 1 1062 kjohnson    7642 2009-08-19 12:01 role_data.db.gz
    -rwxrwxrwx 1 1062 kjohnson 1044368 2009-04-30 12:11 tchar.db.gz

    So there may be an issue there.. not sure.

     
  • Michael Torres

    Michael Torres - 2010-11-09

    I am having the same issue, I have recently installed the latest version of Manatee and when I want to check the "Annotation tool" link, I got this message in my web browser

    Content-Type: text/html; charset=ISO-8859-1
    Can't tie lookup file - : at Manatee/ChadoManateeDB.pm line 4070. Home  |  Help

    ERROR! Can't tie lookup file - : at Manatee/ChadoManateeDB.pm line 4070.
    Error Type
    Description
    Support If you need help with this error please submit a request by going to Manatee at SourceForge and clicking on "Submit bugs" at the bottom of the page.

    Looking at my apache log error

    ann_tools.cgi: MLDBM error: Second level tie failed, "" at Manatee/ChadoManateeDB.pm line 4070
    ann_tools.cgi: Can't tie lookup file - :  at Manatee/ChadoManateeDB.pm line 4070.

    Now about the permission for all lookup files were changed between 777 and 775, besides I've been changing ownership I did it with root, apache and my personal account. None worked…I hope anyone can help me with this.

     
  • Todd Creasy

    Todd Creasy - 2010-11-09

    mike-bioinfo

    Hang in there for just a couple of days.  I'm going to be making a whole new release that will resolve this issue (among others).  Hopefully done by Friday at the latest!

    todd

     
  • Todd Creasy

    Todd Creasy - 2010-11-16

    Just an FYI, I'm going to be working on this release today.  Apologies for the delay…

     
  • Todd Creasy

    Todd Creasy - 2010-11-22

    I just update SourceForge with a new release. 

    manatee-2.15.1_linux.tgz

    I did this rather quickly so please let know if you have problems.  A few issues:

    - I realized after the fact that I didn't update the README file so follow these instructions and you "should" be ok. 
    - Also, keep in mind that this is linux only.  Mac is coming later.
    - MLDBM lookup databases are platform-specific.  I created the dbs on a 64-bit linux system.  If you're using a 32-bit system, there might be problems.  If that's the case, let me know and I'll try and get a 32-bit Ubuntu VM up on my laptop and recreate the lookup databases.

    - Instructions (Make sure you have admin privileges on your system for Apache AND MySQL)

    1. src - Manatee's source code
    - perl Makefile.PL (follow the instructions)
    - make
    - make install

    2. databases - this will install the new MySQL databases and the MLDBM lookup files
    - perl Makefile.PL (follow the instructions
    - make
    - make install
    --> The database install for uniprot_annotation will take a very long time.  After the make install, go on a coffee break :)

    3. Change the Manatee.conf file in …cgi-bin/chado_prok_manatee/conf/Manatee.conf

    Let me know if you have ANY problems at all.  I'm going to spend some time next week updating the documentation and working on a Mac install.

    todd

     
  • Michael Torres

    Michael Torres - 2011-02-22

    Hi Todd,

    I've downloaded this new release, but when I am trying to install the DB I got this error

    "Installing database lookup files to /home/Path/to/my/lookup_files/…
    cp: cannot stat `lookups/*.db.gz': No existe el fichero o el directorio
    make: ***  Error 1"

    Where are this lookups files in this new release? Do I have to use the old ones?

     
  • Michael Torres

    Michael Torres - 2011-02-22

    Hi todd,

    Nevermind I could handle this problem changing Paths and privileges to those files…

    Cheers

     
  • Todd Creasy

    Todd Creasy - 2011-02-22

    Awesome.  There's a new release too but we JUST found a small problem.  However, I don't think it will affect anyone here so far.  It's only with large annotation databases.  I have someone working pretty much full time on Manatee now so you should start to see more releases AND documentation with release notes!  Unheard of in my world :)

    Anyway, there's a new lookup files that handles the uniprot_annotation database (rather than using the database itself).  It's much faster to do it this way.  The lookup file is large so we split it from the main download and will have to be downloaded separately.  It takes a long time so be advised.

    Thanks,

    todd

     
  • Michael Torres

    Michael Torres - 2011-02-22

    Hi Todd,

    Sorry to bother you again, I could handle to install properly but when I try to log in I had this error

    "Can't open /pathways/config/pathway_map.tab (No such file or directory) at ../shared/Manatee/PathwayToolsLinks.pm line 110. "

    I don't know where is this "pathway_map.tab" file and that's why I didn't update the conf file with the correct pathway. Could please tell me where can I find it?

    Cheers

     
  • Todd Creasy

    Todd Creasy - 2011-02-22

    Uh oh.  That was missed.  I'm sorry.  Let me upload a conf file and I'll point you to it.  Put it in the same directory as your Manatee.conf file and point to that location IN the Manatee.conf file for the PATHWAY_TOOLS_CONFIG variable.

     

     
  • Todd Creasy

    Todd Creasy - 2011-02-22

    I put a conf file called pathway_map.tab in igs_manatee / 2.21.1.  Download it and put it where I indicated in my previous post.  Let me know if that works.  We'll have to address this issue over here ASAP.

    todd

     
  • Michael Torres

    Michael Torres - 2011-02-22

    Now it works but, I have this error when I try to use "Annotation tools" and then submit "all genes, ordered by role category"

    "You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1"

    I am using the latest release of mysql running in OpenSuse 11.1 with greenlive update.

    And another error is when I try to look por a particular gene for example: cgsp_2887 . I got this:

    Can't tie lookup file - /Path/to/my/lookup_fileshmm_go.db: No such file or directory at ..//Manatee/ChadoManateeDB.pm line 4467.

    I have noticed there's a missing " / " to complete the path that's why it couldn't find the "hmm_go.db" …How can I correct this error?

    Cheers

     
  • Todd Creasy

    Todd Creasy - 2011-02-22

    You need to make sure all paths in the Manatee.conf file are updated.  The "/Path/to/my/lookup_files" is just a placeholder.  You must change it to the path where each lookup files is located.  Let me know if this isn't the problem. 

     
  • Todd Creasy

    Todd Creasy - 2011-02-22

    I would also recommend you forgo the 2.10.1-beta and use 2.21.1.  If there's fixes to be made, it will be easier (and safer) for you to upgrade from that release. 

     
  • Michael Torres

    Michael Torres - 2011-02-24

    Hi todd

    I have updated everything and corrected the first error, but I am still having this issue when I try to look for a single gene:

    ERROR! You have an error in your SQL syntax; check the manual that corresponds to your MySQL server version for the right syntax to use near '' at line 1
    Error Type SQL/Database
    Description There is a query that could not be executed. Please check the query syntax, arguments, and database schema
    Database cgsp
    Failed Query SELECT DISTINCT t.uniquename, '', fp2.value, fp3.value, fp4.value, fl.fmin, fl.fmax, fp.value, fp5.value, '', '270', 'Disrupted reading frame', 'Frameshifts', fl.strand, a.uniquename, d2.accession FROM feature a, featureloc fl, dbxref d2, db db2, feature_dbxref fd2, feature g, feature_relationship tg, organism o, feature_relationship tf, feature fs, feature t LEFT JOIN featureprop fp ON (t.feature_id = fp.feature_id AND fp.type_id = 52) LEFT JOIN featureprop fp2 ON (t.feature_id = fp2.feature_id AND fp2.type_id = 132) LEFT JOIN featureprop fp3 ON (t.feature_id = fp3.feature_id AND fp3.type_id = 131) LEFT JOIN featureprop fp4 ON (t.feature_id = fp4.feature_id AND fp4.type_id = 130) LEFT JOIN featureprop fp5 ON (t.feature_id = fp5.feature_id AND fp5.type_id = 49) WHERE t.feature_id = fl.feature_id AND fl.srcfeature_id = a.feature_id AND t.feature_id = tg.subject_id AND tg.object_id = g.feature_id AND g.feature_id = fd2.feature_id AND fd2.dbxref_id = d2.dbxref_id AND d2.db_id = db2.db_id AND db2.name = 'TIGR_moore' AND d2.version = 'locus' AND t.type_id = 23813 AND g.type_id = 23844 AND a.type_id = 23493 AND tg.type_id = 7 AND t.organism_id = o.organism_id AND o.common_name != 'not known' AND t.is_obsolete = 0 AND t.feature_id = tf.object_id AND tf.subject_id = fs.feature_id AND fs.type_id =
    Query Arguments
    Support If you need help with this error please submit a request by going to Manatee at SourceForge and clicking on "Submit bugs" at the bottom of the page.
    Other Links Back to login page  |  View raw error output

    I don't know what it means. Could please help with this issue?

    Cheers

     
  • Todd Creasy

    Todd Creasy - 2011-02-24

    Ugh.  We're really forgetting a lot of crap.  The reason you get the failure is b/c the cgsp database you have is an older version and is missing some data that the newer query requires.  What I've done is uploaded a new database file to the 2.21.1 folder called cgsp.ddl.gz and also analyze.ddl.gz.  Here's what you want to do:

    1. Login to your mysql from the command line:

    mysql> drop database cgsp;
    mysql> create datdabase cgsp;
    mysql > exit

    shell> zcat cgsp.ddl.gz | mysql -h -u -p -D cgsp
    shell> zcat analyze.ddl.gz | mysql -h -u -p -D cgsp

    The first command will install the new data into cgsp.  The 2nd command runs a quick indexing query to speed up querying in cgsp. 

    We are creating a new release now that addresses this issue and the pathways.tab issue too.  I'm sorry for the troubles.

    todd

     
  • DavE

    DavE - 2011-04-25

    Hi,
    Im david from india. i have a problem with the installing manatee. its been a week since i started looking out for a proper installation manual for manatee and i swear if i find it im gonna post in a blog for the future users.:) let me get to the point. i have biolinux installed in my 64 bit machine. i need a manual for installation. can u help me out with the basics? since im new to linux and im  a rookie in programming i need a little push:) so wat are all the prerequisites for manatee installation? i have installed postgres, mysql RBDMS. i have a porblem with the apache installation too.. kindly help me out.. looking forward for your kind reply. thanks.

     
  • Todd Creasy

    Todd Creasy - 2011-04-25

    Umm…  There's been an install doc there for a very long time now.  It's under "Installation Instructions" right on the front page.  I think that's a pretty sensible location.  There's also a README under Documentation.  You can post that on a blog.

    I think you need to read over that document first before I try and help you.  Your questions are extremely vague and it would be difficult for me to try and help you with everything.  It might not be the best documentation, but it is certainly sufficient.

    todd

     

Log in to post a comment.

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks