tag:blogger.com,1999:blog-8584629468471803075.post7050942471321517101..comments2024-01-31T12:30:28.282+00:00Comments on Blasted Bioinformatics!?: BLAST+ memory hog with subject FASTA and XML outputPeter Cockhttp://www.blogger.com/profile/00233221181317137855noreply@blogger.comBlogger4125tag:blogger.com,1999:blog-8584629468471803075.post-91881602850863937552020-04-11T14:44:25.654+01:002020-04-11T14:44:25.654+01:00Hey guys, any idea why blastx load all files (db a...Hey guys, any idea why blastx load all files (db and query) in RAM memory, run threads number specified for some seconds, flush memory RAM, reload all files again, run threads again for some seconds, reflush... repeating a circle? This spends a long unnecessary time... How to solve this problem?rthttps://www.blogger.com/profile/17638980049061919818noreply@blogger.comtag:blogger.com,1999:blog-8584629468471803075.post-23131182301697733662012-09-15T01:05:48.212+01:002012-09-15T01:05:48.212+01:00I have run many blasts with xml output. The bigges...I have run many blasts with xml output. The biggest problem that I have seen with xml is that the program seems to hold all of the output in memory until the run is completely finished. This is why you didn't have any output in your xml file when your run failed. I am not sure why the programs work this way, but I would love to know if there is a way to change this behavior.WayToBeAStereotypehttps://www.blogger.com/profile/07190970172718889175noreply@blogger.comtag:blogger.com,1999:blog-8584629468471803075.post-23950269660305955432012-05-21T05:20:03.416+01:002012-05-21T05:20:03.416+01:00Any idea how this approach compares to the old bl2...Any idea how this approach compares to the old bl2seq in BLAST legacy i.e. (http://nebc.nerc.ac.uk/bioinformatics/docs/bl2seq.html)<br /><br />I presume this would have been based off that, which to my knowledge does not internally produce a BLAST database.Nabilhttps://www.blogger.com/profile/18355949983002211437noreply@blogger.comtag:blogger.com,1999:blog-8584629468471803075.post-62185748635428881912012-04-23T00:15:27.940+01:002012-04-23T00:15:27.940+01:00As far as I'm aware, only one of the three sta...As far as I'm aware, only one of the three stages in blast are hyperthreaded. I too have not found threading to give much overall speed increase. So its still worth splitting your query file into smaller chunks and running them in parallel.Nathan Watson-Haighhttps://www.blogger.com/profile/04644217548765097983noreply@blogger.com