Blastall Fatal Error Failed To Allocate
and workaround for NCBI BLAST "Failed to allocate" error. title:BLAST "Failed to allocate" error I have not seen The BLAST segment fault or memory allocation bug with 64 bit executables (of course running on a 64 operating system). With very large libraries such as refseq genomic, loading the full search fatal error : failed to allocate memory. out of virtual memory. library takes more than 2GB of RAM (the address limit for 32 bits). The fatal error aborting the dtm process due to memory allocation failure informatica message appears to refer to the amount of additional RAM that can't be allocated, rather than the total amount currently used or currently requested. A partially effective workaround is to only use one "volume" of a database. (search library). For instance use refseq_genomic.00 or refseq_genomic.01. The workaround helps with blastn, but only helps in half the cases with tblastx. tblastx seems to segment fault about half the time when searching against refseq_genomic, even when only searching one section of the NCBI Blast library. Not surprisingly, the size of the NCBI volumes is around 1GB (compressed). Subsequent testing showed that using a single, smaller library volume, roughly 400MB, did not cause the crash. I downloaded all of refseq genomic (aka "complete"), and built my own Blast search library with commands such as: cat *.fna > complete.fasta /bioinfo/blast/bin/formatdb -i complete.fasta -p F -o T -n refseq_genomic -v 1600 (On my hardware, I think the cat command took 30 minutes. The resulting file "complete.fasta" was around 105GB.) In all my test cases, the query sequence is short. ulimit is unlimited. The problem occurs only 32 bit systems. With further testing, we have found that using the 64 NCBI Blast executables with a 64 bit operating system do not have this bug. Instead of using one command with -d such as: /my_libs/refseq_genomic_20090630/refseq_genomic run several searches where -d is: /my_libs/refseq_genomic_20090630/refseq_genomic.00 /my_libs/refseq_genomic_20090630/refseq_genomic.01 /my_libs/refseq_genomic_20090630/refseq_genomic.02 A work around would be to set up the Perl script you use to run BLAST to iterate over the set of database volumes. (NCBI is not clear that .00, .01, .02, etc. are "volumes", but the word "volume" is used in the help text for formatdb, so I'll go with that nomenclature.) Below are typical command lines and error messages. zeus is 32 bit Linux. hera is 64 bit Apple OSX running the 32 bit NCBI executable (As of this writing there is no 64 bit OSX executable from NCBI.) [zeus ~]$ /bioinfo/blast-2.2.18/bin/blastall -i blast_input.fasta -p blastn -F "T" -m 7 -T T -e 1e-10 -v 50 -b 50 -M BLOSUM62 -A 0 -a 1 -d "/search_libs/refseq_genom
faq • rss Community Log In Sign Up Add New Post Question: Problem Running Blast Jobs. 2 5.5 years ago by Anjan • 630 United States Anjan • 630 wrote: I started to run blast, locally on my machine, on 4 files with 1323, 210, 501, 166 fasta sequences each. For all jobs except the first one blast returned an error: blastall(7004) malloc: *** mmap(size=2097152) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug The first http://defindit.com/readme_files/blast_failed_to_allocate.html job is currently still running as I'm writing this. The exact blastall command used is as follows: blastall -p blastn -d /Users/anjan/blastdb/nt -i
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a mpiblast run really take this long? Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Arvind, I couldn't tell much from the debug output. Could you try the following configurations to see if it will work? 1) -b 1 -v 1 -m 8 (remove -F option) 2) -b 1 -v 1 -m 8 --output-search-stats Thanks, Heshan On Sep 23, 2008, at 4:32 PM, ThirumalaiswamySekhar, Arvind (A) wrote: > Hello > > I am attaching the log files from the debug option of mpiBLAST. The > program terminates with the bailing out error or sometimes the > std9alloc > error randomly. > > I am using the following options > > -b 1 -v 1 -m 8 -F "" to restrict the results to 1 hit per sequence and > report the results in tabular format. (this should be lesser data than > the actual blast). > > Kindly let me know about your suggestions to tackle this problem. > > Sincerely > Arvind > > > > -----Original Message----- > From: users-bounces at lists.mpiblast.org > [mailto:users-bounces at lists.mpiblast.org] On Behalf Of > ThirumalaiswamySekhar, Arvind (A) > Sent: Monday, September 22, 2008 8:38 AM > To: Heshan Lin; mclaesson at bioinfo.ucc.ie > Cc: users at lists.mpiblast.org > Subject: Re: [mpiBLAST-Users] should a mpiblast run really take this > long? > > Hello all, > > I have been out over the weekend and hence the hiatus. Apologies. I > noticed the following behavior with mpiBLAST. > > When I use an input file with just two sequences in it, I get the > st9alloc problem and after a few runs sometimes the bailing out with > error message. This happens all the time when I use "tblastn". > > However with the same database, if I use a file with 1000 sequences > and > the blast flavor "blastn" instead of tblastn, the program works fine > without any errors at all. "blastp" works fine too. I will try to get > the debug file to you guys at the earliest. > > Thank you > Sincerely > Arvind > > > > -----Original Message----- > From: users-bounces at lists.mpiblast.org > [mailto:users-bounces at lists.mpiblast.org] On Behalf Of Heshan Lin > Sent: Saturday, September 20, 2008 10:49 PM > To: mclaesson at bioinfo.ucc.ie > Cc: users at lists.mpiblast.org > Subject: Re: [mpiBLAST-Users] should a mpiblast run really take this > long? > > Marcus, > > I noticed that you used very larg