formatdb error no database name was specified Quicksburg Virginia

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formatdb error no database name was specified Quicksburg, Virginia

juberpatel commented Jul 11, 2013 sure. If GI numbers are included and more than one sequence has the same GI number, formatdb terminates with an error. juberpatel commented Jul 11, 2013 the command is: cd "/home/juber/"; ChimeraSlayer.pl --exec_dir "/tmp" --query_NAST "test_chimera_slayerym3HcCqWTRq4zmiBKwoh.txt" > "/tmp/tmpUXqGENP0RaON0VNyKv5n.txt" 2> "/tmp/tmpGiVPbmXDu4oGzscelbxC.txt" The run with normal and sudo privileges produces these errors: [email protected]:~$ [email protected]:~$ If the database connection is successful, you will then be shown a message dialog "No Users in Database.

drwxr-xr-x 7 root root 4096 Apr 29 2010 .. -rw-r--r-- 1 root root 30 Apr 29 2010 Makefile drwxr-xr-x 4 root root 4096 Apr 29 2010 RDP -rw-r--r-- 1 root root These will allow retrieval of individual sequences by utilities like fastacmd. -v Database volume size in millions of letters [Integer] Optional default = 0 range from 0 to This option breaks this is very strange. biocore member jairideout commented Jul 11, 2013 You might try rerunning the unit test to see if it passes, now that you have the blast-formatted databases: python /opt/qiime/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py ChimeraSlayerChimeraCheckerTests.test_chimeraSlayer_identify_chimeras_default_ref_db Those formatdb

Save this archive into the patimdb_XXXXXXXX/apps subdirectory of your PATIMDB distribution. This time, enter the DBPASSWORD. CREATE DATABASE DBNAME; If this command succeeds, you have just created an empty database with no tables. ok test_clearcut_supported_version (__main__.Qiime_config) clearcut is in path and version is supported ...

To do this, open the file /opt/qiime/qiime-1.7.0-release/lib/qiime/identify_chimeric_seqs.py and go to line 616. Usually results will be at least as good or better (in terms of score/evalue) than the results of corresponding individual queries; exceptions occur due to the heuristic nature of BLAST. This step also requires that you have a functioning installation of the mysql database server and text-based client and that you also have the privelege to log into the MySQL RDBMS Make sure the location indicated in the Analysis Settings Window is correct.

If one uses "-F T" then normal filtering by seg or dust (for blastn) occurs (likewise "-F F" means no filtering whatsoever). ok test_working_dir (__main__.Qiime_config) working_dir, if set, is set to a valid path ... To convert a text GI file to binary, use the following command: formatdb -F text_gi_list -B binary_gi_list -F [file]Default: Optional Specifies a GI file, either text or binary. However, The collection of sequences passed to formatrpsdb must already be consistent in several important ways: - All sequences must use the same protein alphabet. - All scores in all PSSMs

For convenience, it comes as a compressed tar archive (.tgz) by the name of patimdb_XXXXXXXX.tgz or as a zip archive by the name of patimdb_XXXXXXXX.zip, where XXXXXXXX is the release date. I just recently installed qiime 1.7.0 on Ubuntu 13.04 using the qiime-deploy tool and I am still seeing this issue, even though lines 609-610 in identify_chimeric_seqs.py have been modified as described On Linux, you need to install the mysql-server, the mysql-client, and the mysql-shared libraries package. (These packages may be named slightly differently on different distributions.) On MacOS X, you only need Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » View Posts Latest Open RNA-Seq ChIP-Seq SNP Assembly Tutorials Tools Jobs Forum Planet All » Home

ok test_muscle_supported_version (__main__.Qiime_config) muscle is in path and version is supported ... ok test_numpy_suported_version (__main__.Qiime_config) numpy version is supported ... ok test_chimeraSlayer_install (__main__.Qiime_config) no obvious problems with ChimeraSlayer install ... It sounds like on my system, ChimeraSlayer.pl is finding this database, but it isn't on yours.

If not, do you know who might help with this? Change the line from: app = ChimeraSlayer(params=params, HALT_EXEC=HALT_EXEC) to: app = ChimeraSlayer(params=params, HALT_EXEC=True) Then open the file /opt/qiime/qiime-1.7.0-release/tests/test_identify_chimeric_seqs.py and go to line 253. If you intend to install MySQL on a recent RPM-based distribution of Linux, you can simply install the MySQL RPMs that came with your operating system or use the yum utility How To Capture The Blast Result In A String Variable To Save In A Database Using Bioperl I am trying to run RemoteBlast using the Bio::Tools::Run::RemoteBlast object of BioPerl.

To check that the blastall executables actually works, execute cd to the blast-VERSION/bin subdirectory and type the command: ./blastall If the output is a (long) summary of the proper usage of Sequence Similarity4.1 Introduction to Information Theory4.2 Amino Acid Similarity4.3 Scoring Matrices4.4 Target Frequencies, lambda, and H4.5 Sequence Similarity4.6 Karlin-Altschul Statistics4.7 Sum Statistics and Sum Scores4.8 Further ReadingPart III: PracticeChapter 5. Academic institutions wishing to script phred or run it as command line program only (as the PATIMDB application requires) may request a free restricted license. The following settings should be checked: Blast Executable Formatdb Executable Phred Executable Phred Parameter File If the blastall, formatdb, and phred executables are located within your executable path, you can leave

ok test_raxmlHPC_supported_version (__main__.Qiime_config) raxmlHPC is in path and version is supported ... From looking at the ChimeraSlayer.pl code, it checks whether there is a blast-formatted database present in the same directory as the rRNA16S.gold.fasta file, and will skip the formatdb step if it ok test_pynast_template_alignment_fp (__main__.Qiime_config) pynast_template_alignment, if set, is set to a valid path ... The Cancel button exits the program.

For the sake of this procedure we will use DBNAMEYou will also want to pick a user name and password. As you can see in the above output, they were not present before the sudo run. ok test_denoiser_supported_version (__main__.Qiime_config) denoiser aligner is ready to use ... Within the archive, you should find a .jar file by the name of mysql-connector-java-[version]-bin.jar.

After the archives contents are extracted, cd to the blast-VERSION\bin subdirectory and execute blastall.exe. I have heard from a colleague about some compatibility issue for UCHIME output, I still have to check it first hand. … On Wed, Jul 10, 2013 at 3:42 PM, Jai I am trying to replace BL... biocore member jairideout commented Jul 11, 2013 Thanks- can you also post the output of running ChimeraSlayer.pl?

You can check if they are in your path by simply invoking them from a command line in an terminal or a command prompt window. ok test_blastmat_dir (__main__.Qiime_config) blastmat_dir is set to a valid path. ... While it is generally straightforward to install the MySQL database server, there are sometimes pitfalls, depending on what version of MySQL you are installing, and on what host operating system. These values are described in great detail in PATIMDB Application Configuration Window Help.

You may specify that input come from stdin with -i stdin, but you must also set the -n parameter to give it a name. ok test_R_supported_version (__main__.Qiime_config) R is in path and version is supported ... I think the AMIs are using Ubuntu 11.x (not sure what version exactly), so things are passing there as well. @juberpatel can you try running the following command: ChimeraSlayer.pl You should The PATIMDB Application Configuration window is the interface where parameters are entered for connection to the database.

The second group of files contains precomputations used to speed up RPS Blast searches of the standard protein database. Under MacOS X, Linux, and Unix, this is done in a terminal window. Multiple database names (bracketed by quotations) will be accepted. Table 1 Host Computer Software Vendor (URL) Desktop Workstation Java 2 Platform Standard Edition (J2SE)Version 5.0 Windows and Linux: Sun (java.sun.com/javase/) MacOS X: Apple( http://developer.apple.com/java/download/) Desktop Workstation MySQL Connector/J, Version 3.0.15

These dependencies are summarized in Table 1 below.