clc genomics workbench blast at ncbi not working

#CLC GENOMICS WORKBENCH BLAST AT NCBI NOT WORKING SOFTWARE#

Running multiple blast searches simultaneouslyįor much of the time during a search, BLAST+ programs do not use all threads available. For a blastx search, look for a running process with the name blastx. For example, if you ran a blastn search, look for a running process with the name blastn. The BLAST executables have the same name as the type of blast search launched. If you are concerned about whether a blast job you launched from the CLC Workbench is still running, please try checking for the relevant executable among the processes your machine is running.Ĭhecking the running processes on a system can be done using the Task Manager (Windows), Activity Manager (Mac) or checking the process table (Linux). When you launch a local blast job on a CLC Workbench or CLC Genomics Server, an NCBI BLAST+ program is run on your local system in the background for the actual searching.

#CLC GENOMICS WORKBENCH BLAST AT NCBI NOT WORKING SOFTWARE#

In our experience running BLAST searches, via CLC software or using NCBI BLAST+ commands directly, if disks where the databases are stored are very busy, a search that takes only a few minutes at quiet times can take up to hours when demand on the disks is very high. How busy the disks where the databases are stored are.The tblastx and tblastn searches will take even longer for similar reasons. For example, blastx searches take much longer than blastn searches as the entire query set has to be translated in 6 frames and then a search for each of those frames is executed. The type of BLAST search you are running.The specifics of this depend on your exact search, for example searching with many small sequences may scale better than searching with a few large sequences. Please note however, beyond 4 to 6 threads, you may not see much benefit in speed. The default number of threads specified in the Workbench is the number of cores on your machine. The parameter choices, such as the number of threads you specified, the word size, expect value and number of hits to be reported.The size of the database you are searching.how much sequence data is there, and also the nature of your query set a few very large sequences can take longer than many smaller sequences.

How long a BLAST job takes to run depends on many things, including: What can affect the speed of a local blast search? When your BLAST search takes a long time, it is likely that it is still running as expected. Why are my local BLAST searches taking so long?

Clc genomics workbench blast at ncbi not working