Activity for ConsPred
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Thomas Rattei posted a comment on discussion General Discussion
Hi Gyeongjun Cho, the Conspred development has been ended with version 1.33 (except minor bug fixes). We are currently developing a completely rewritten Conspred2, which focuses on consensus gene prediction and high-quality gene start prediction. Conspred2 will not do any functional annotation (consider e.g. Prokka and GAMOLA2 for this purpose). As an alternative, which includes functional annotation, we recommend prokka. It has received an update recently. Best wishes, Thomas
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GyeongjunCho posted a comment on discussion General Discussion
Hi, I am Gyeongjun Cho I can not download. http://fileshare.csb.univie.ac.at/conspred_data/conspred_resources_LATEST.tar.gz thanks.
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Alexander Platzer modified ticket #5
blastp issue
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Calvin Kim posted a comment on ticket #5
Fantastic. I updated BLAST and it works much more smoothly now. Thank you!
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source code for ConsPred2 binary
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integrate the use of fragmental sources
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no further request;
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Have just recognized that this particular error is due to the ncbi blast+ version you are using. 2.2.29 seems to not support the blastp-fast task setting (although the error message claims so). So, either switch to a newer blast+ (2.3.0 works well), or change the conspredProperties.txt setting to: CONSPRED_BLAST_TASK=blastp best, Thomas
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Hi, please check the contents of your conspredProperties.txt file. It should contain a line like CONSPRED_BLAST_TASK=blastp-fast Please check if your modifications in conspredProperties.txt are without errors (use diff to compare a modified version of conspredProperties.txt with the original one), Best, Thomas
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blastp issue
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Afif Elghraoui posted a comment on ticket #4
Great. Thanks for that information!
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Hi, there is another repo for the conspred2 binary source code: https://sourceforge.net/p/conspred2 Please get the sources from there. Best, Thomas
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source code for ConsPred2 binary
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contentual typo in the configs
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ConsPred released /ConsPred_v1.33.tar.gz
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blastGenes declared different
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issue with new labels at one converter
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intermediate change of the config
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resolved label but and generic interpro
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bugfix for the absence of the taxonomy filter
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version change (new version)
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Adapted the code to the new database for 11blas...
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Merge branch 'master' of ssh://git.code.sf.net/...
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made one point in the docu/comments more clear
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changed config
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version change added
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Thomas Rattei committed [de1a73]
Added rules to detect partial ORFs, to not chan...
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removed range-filtering for coordinates
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integrate the use of fragmental sources
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tidied up +1
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++docu for the core module
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Merge branch 'master' of ssh://git.code.sf.net/...
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Minor modifications on the indexing scripts to ...
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docu - removed offline points
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one path/call for interpro was still wrong (fixed)
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exchange of the core modules and slurm update
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=jfrank87 committed [7bacd2]
Modified README: added co-author
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default config changes for the new local cluste...
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Merge branch 'master' of ssh://git.code.sf.net/...
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config for less sources
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Thomas Weinmaier committed [7e6a40]
Cleaned up redundant variables and added comments
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docu++ (in conspredProperties.txt)
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changed config file for cube-use and added seco...
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docu++
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fixed taxonomy as text; especially when contain...
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stepwise merge...
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set README to remote;
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++docu
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Thomas Weinmaier committed [b11e24]
Updated default KEGG path values
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Thomas Weinmaier modified a wiki page
Home
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Thomas Weinmaier committed [0de334]
Adjusted config file path settings for user ins...
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Thomas Weinmaier committed [690aa7]
Set CONSPRED_INSTALLATION_FOLDER to UNDEFINED i...
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Home
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more memory for critica
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fix for version 1.21
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docu++
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check invalid characters in handle in the begin...
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docu++
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updateDatabases++; a config variable changed fo...
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updated environmentPreparation by ThomasR
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updated environmentPreparation by Thomas Rattei;
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readme++
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java source update; changed MergeGff and relate...
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fixed some bugs in MergeGff.jar;
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when more output from mergegff, the calling bas...
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removed the progress indicator and added anothe...
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Thomas Weinmaier committed [2db5ad]
Added missing GeneMark output line
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docu++
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Merge branch 'master' of ssh://git.code.sf.net/...
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removed confusion between 'less than' and '-le'
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Thomas Weinmaier committed [613c45]
Updated eggNOG version
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version..
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version string and Prodigal default to old version
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Thomas Weinmaier committed [338c3c]
Changed version to 1.1.0 according to http://se...
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Thomas Weinmaier committed [6b3280]
Changed output path of summary file to be in ma...
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docu++
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Thomas Weinmaier committed [ff1a73]
Moved critica plausibility check to file combin...
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Thomas Weinmaier committed [0b090b]
Added removal of file conspred_errors.txt in co...
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Thomas Weinmaier committed [ba1504]
Removed SCRATCH folder
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Thomas Weinmaier committed [d6f302]
Added plausibility checks
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Thomas Weinmaier committed [db4a19]
Replaced several WARNING messages in Blast2Gff ...
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config docu++
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