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From: Lorena P. <lor...@gm...> - 2012-02-22 17:16:45
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Hi, could you run without put anything in the frequency greater or less. This number should be integers, 0 if you want to get everything, and maybe 10 if you want to remove sequences with lower than 10 counts. frequency less than, greater than. less than 0.5 and greater than 0.01 it would take nothing. 1 is the minimum. cheers On Wed, Feb 22, 2012 at 2:48 PM, Bruce, Can John <can...@ya...> wrote: > Hi Lo,**** > > ** ** > > The parameters were: group1=testr, Frequency greater=0.5, Frequency > less=0.01, Select miRNA-like DB=miRNA, Contribution Cut Off=10, applied > probabilistic model=zscore, and all checkboxes checked.**** > > ** ** > > By the way, does “frequency less” mean “frequency less than” or “minimum > frequency” ?**** > > ** ** > > Can Bruce**** > > Bioinformatics Resource**** > > Keck Lab**** > > ** ** > > *From:* Lorena Pantano [mailto:lor...@gm...] > *Sent:* Wednesday, February 22, 2012 3:20 AM > *To:* Bruce, Can John > *Cc:* seq...@li... > *Subject:* Re: [Seqbuster-questions] miRNA analysis problem**** > > ** ** > > Hi, **** > > ** ** > > Thank you very much to ask me. I will be out of office during the morning, > but this afternoon I will check the code to see if there is any bug, since > updated last friday maybe I introduce a bug. **** > > ** ** > > One question, did you change any parameter?**** > > ** ** > > I will come back today**** > > ** ** > > cheers**** > > > Lo > > **** > > On Wed, Feb 22, 2012 at 12:39 AM, Bruce, Can John <can...@ya...> > wrote:**** > > Hello,**** > > **** > > I am going through the test data set to familiarize myself with seqbuster. > In the miRNA analysis step I got the following error message in the > IsoseqDistribution.Rout file:**** > > **** > > ==============================**** > > [1] "select > `id`,`chr`,`freq`,`trimmed5`,`trimmed3`,`addition3`,`mut`,`trimmed3ref`,`trimmed5ref` > from `testpro`.`testr` `freq` >= 0.**** > > 01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP > '^0[ACTG]+' AND `mut` NOT REGEXP '^-[0-9]+[ACTG]+' AND `mut`**** > > NOT REGEXP '^[0-9]+[ACTG]+[0-9]+';"**** > > Error in mysqlExecStatement(conn, statement, ...) : **** > > (could not run statement: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL serve**** > > r version for the right syntax to use near '>= 0.01 AND `DB` LIKE 'miRNA' > AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^' at line **** > > 1)**** > > Calls: dbSendQuery ... .valueClassTest -> is -> is -> mysqlExecStatement > -> .Call**** > > Execution halted**** > > ========================**** > > **** > > Am I doing something wrong? is there a "WHERE" missing in the SQL query > above?**** > > **** > > **** > > Can Bruce**** > > Bioinformatics Resource**** > > Keck Lab**** > > Yale University**** > > **** > > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Seqbuster-questions mailing list > Seq...@li... > https://lists.sourceforge.net/lists/listinfo/seqbuster-questions**** > > ** ** > |
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From: Bruce, C. J. <can...@ya...> - 2012-02-22 13:48:33
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Hi Lo, The parameters were: group1=testr, Frequency greater=0.5, Frequency less=0.01, Select miRNA-like DB=miRNA, Contribution Cut Off=10, applied probabilistic model=zscore, and all checkboxes checked. By the way, does "frequency less" mean "frequency less than" or "minimum frequency" ? Can Bruce Bioinformatics Resource Keck Lab From: Lorena Pantano [mailto:lor...@gm...] Sent: Wednesday, February 22, 2012 3:20 AM To: Bruce, Can John Cc: seq...@li... Subject: Re: [Seqbuster-questions] miRNA analysis problem Hi, Thank you very much to ask me. I will be out of office during the morning, but this afternoon I will check the code to see if there is any bug, since updated last friday maybe I introduce a bug. One question, did you change any parameter? I will come back today cheers Lo On Wed, Feb 22, 2012 at 12:39 AM, Bruce, Can John <can...@ya...<mailto:can...@ya...>> wrote: Hello, I am going through the test data set to familiarize myself with seqbuster. In the miRNA analysis step I got the following error message in the IsoseqDistribution.Rout file: ============================== [1] "select `id`,`chr`,`freq`,`trimmed5`,`trimmed3`,`addition3`,`mut`,`trimmed3ref`,`trimmed5ref` from `testpro`.`testr` `freq` >= 0. 01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^0[ACTG]+' AND `mut` NOT REGEXP '^-[0-9]+[ACTG]+' AND `mut` NOT REGEXP '^[0-9]+[ACTG]+[0-9]+';" Error in mysqlExecStatement(conn, statement, ...) : (could not run statement: You have an error in your SQL syntax; check the manual that corresponds to your MySQL serve r version for the right syntax to use near '>= 0.01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^' at line 1) Calls: dbSendQuery ... .valueClassTest -> is -> is -> mysqlExecStatement -> .Call Execution halted ======================== Am I doing something wrong? is there a "WHERE" missing in the SQL query above? Can Bruce Bioinformatics Resource Keck Lab Yale University ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ Seqbuster-questions mailing list Seq...@li...<mailto:Seq...@li...> https://lists.sourceforge.net/lists/listinfo/seqbuster-questions |
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From: Lorena P. <lor...@gm...> - 2012-02-22 08:20:25
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Hi, Thank you very much to ask me. I will be out of office during the morning, but this afternoon I will check the code to see if there is any bug, since updated last friday maybe I introduce a bug. One question, did you change any parameter? I will come back today cheers Lo On Wed, Feb 22, 2012 at 12:39 AM, Bruce, Can John <can...@ya...>wrote: > Hello,**** > > ** ** > > I am going through the test data set to familiarize myself with seqbuster. > In the miRNA analysis step I got the following error message in the > IsoseqDistribution.Rout file:**** > > ** ** > > ==============================**** > > [1] "select > `id`,`chr`,`freq`,`trimmed5`,`trimmed3`,`addition3`,`mut`,`trimmed3ref`,`trimmed5ref` > from `testpro`.`testr` `freq` >= 0.**** > > 01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP > '^0[ACTG]+' AND `mut` NOT REGEXP '^-[0-9]+[ACTG]+' AND `mut`**** > > NOT REGEXP '^[0-9]+[ACTG]+[0-9]+';"**** > > Error in mysqlExecStatement(conn, statement, ...) : **** > > (could not run statement: You have an error in your SQL syntax; check the > manual that corresponds to your MySQL serve**** > > r version for the right syntax to use near '>= 0.01 AND `DB` LIKE 'miRNA' > AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^' at line **** > > 1)**** > > Calls: dbSendQuery ... .valueClassTest -> is -> is -> mysqlExecStatement > -> .Call**** > > Execution halted**** > > ========================**** > > ** ** > > Am I doing something wrong? is there a "WHERE" missing in the SQL query > above?**** > > ** ** > > ** ** > > Can Bruce**** > > Bioinformatics Resource**** > > Keck Lab**** > > Yale University**** > > ** ** > > > ------------------------------------------------------------------------------ > Keep Your Developer Skills Current with LearnDevNow! > The most comprehensive online learning library for Microsoft developers > is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, > Metro Style Apps, more. Free future releases when you subscribe now! > http://p.sf.net/sfu/learndevnow-d2d > _______________________________________________ > Seqbuster-questions mailing list > Seq...@li... > https://lists.sourceforge.net/lists/listinfo/seqbuster-questions > > |
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From: Bruce, C. J. <can...@ya...> - 2012-02-21 23:39:55
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Hello, I am going through the test data set to familiarize myself with seqbuster. In the miRNA analysis step I got the following error message in the IsoseqDistribution.Rout file: ============================== [1] "select `id`,`chr`,`freq`,`trimmed5`,`trimmed3`,`addition3`,`mut`,`trimmed3ref`,`trimmed5ref` from `testpro`.`testr` `freq` >= 0. 01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^0[ACTG]+' AND `mut` NOT REGEXP '^-[0-9]+[ACTG]+' AND `mut` NOT REGEXP '^[0-9]+[ACTG]+[0-9]+';" Error in mysqlExecStatement(conn, statement, ...) : (could not run statement: You have an error in your SQL syntax; check the manual that corresponds to your MySQL serve r version for the right syntax to use near '>= 0.01 AND `DB` LIKE 'miRNA' AND `chr` NOT LIKE 'amb' AND `mut` NOT REGEXP '^' at line 1) Calls: dbSendQuery ... .valueClassTest -> is -> is -> mysqlExecStatement -> .Call Execution halted ======================== Am I doing something wrong? is there a "WHERE" missing in the SQL query above? Can Bruce Bioinformatics Resource Keck Lab Yale University |
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From: Lorena P. <lor...@gm...> - 2011-12-21 17:59:15
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Dear Grazy, sorry very much to answer to late, I missed this email. You comment the following error: "Error: send log file inside seqbuster folder to lorena.pantano@...:Cannot load connection class because of underlying exception: 'java.lang.NumberFormatException: For input string "3306:3306"'.com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException:Cannot load connection class because of underlying exception: 'Java.lang.numberFormatException: For input string "3306:3306"'." But seems very weird. Have you tried to create a project like test2.... did you project stated with a number? thanks Lorena |
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From: Lorena P. <lor...@gm...> - 2011-12-21 17:49:39
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Hi, I would need some more info. Are you using the window interfance or the command line? If it is window interface, you first need to upload the sequences using the trimmed data, and the annotate to the miRNAs. Please give information about what version, what machine are you using, SO, exactly the steps you did until get there... thanks Lorena |
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From: Robin M. <rob...@gm...> - 2011-12-21 11:17:13
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Dear Seqbuster The program seem to be stuck in the miRNA detection-step. I have as input a 40mb collapsed miRNA-read-file like this: >1 GTTTCCGTAGTGTAGTGGTTATCACGTTCGCCT >2 GTTTCCGTAGTGTAGTGGTTATCACGTTCGCC >3 However, I am unable to find hsa as species-option. Do you think this is the reason for the slow processing? Best,Robin |
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From: Gracy <z....@ik...> - 2011-12-13 10:02:30
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Hi Seqbuster team, I work in the Institute of Clinical Molecular Biology in Kiel, Germany. Your tool seems to be very useful for our research. I have downloaded your seqbuster package with the product version 2.0. I have installed all the dependencies and I went through the guided databases installation, and it seems that MySQL runs fine. But when I start to create a new project, after entering the project name (which only contains alphanumeric characters and has the length 8), a error message pops up says: "Error: send log file inside seqbuster folder to lor...@cr...: Cannot load connection class because of underlying exception: 'java.lang.NumberFormatException: For input string "3306:3306"'. com.mysql.jdbc.exceptions.jdbc4.MySQLNonTransientConnectionException:Cannot load connection class because of underlying exception: 'Java.lang.numberFormatException: For input string "3306:3306"'." Can you please tell me what the problem is and how to fix that? Best, Gracy -- M. Sc. Zhipei Gracy Du Institute of Clinical Molecular Biology Christian-Albrechts-University Schittenhelmstr. 12 Haus Niemannsweg 11 D-24105 Kiel Tel.: +49 (0)431-597-1305 eMail: z....@ik... www.ikmb.uni-kiel.de |
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From: lo <lor...@gm...> - 2011-04-22 20:31:14
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Post any bugs, quesition... here -- ########################################### 7th ISCB Student Council Symposium 2011 Friday, July 15th Vienna, Austria http://symposium.iscbsc.org/content/home ########################################### Lorena Pantano PhD Student in Bioinformatics Genes and Diseases Group, CRG http://web.me.com/lorenapantano |
