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Old 12-10-2013, 03:06 AM   #1
bfantinatti
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Location: Sao Paulo/Brazil

Join Date: Aug 2012
Posts: 22
Default Blast2 - Segmentation Fault

Hi guys,
I am having a problem with blast2.
I am running linux mint 14, and installed blast2 using the repository.
It worked fine once, but after the first usage, started to present the following problem:

Any one there had this problem?

My input is:
blast2 -p blastn -i HPRT -d M_zebra_v0.assembly.fasta -o HPRT.Mzebra.out -a 4

The program return this:
*** glibc detected *** blast2: double free or corruption (fasttop): 0x00007f2c6a081f70 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7f2c66453b96]
/usr/lib/x86_64-linux-gnu/libncbi.so.6(Nlm_MemFree+0xe)[0x7f2c669d3c3e]
/usr/lib/x86_64-linux-gnu/libncbi.so.6(ReleaseAppErrInfo+0x70)[0x7f2c669ce6b0]
/usr/lib/x86_64-linux-gnu/libncbi.so.6(Nlm_ReleaseAppContext+0x56)[0x7f2c669d1f26]
blast2(NlmThreadExit+0x78)[0x7f2c67fc23e8]
blast2(+0x64b7)[0x7f2c67fc24b7]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x7e9a)[0x7f2c6679ce9a]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f2c664c93fd]
======= Memory map: ========
7f2c38000000-7f2c38021000 rw-p 00000000 00:00 0
7f2c38021000-7f2c3c000000 ---p 00000000 00:00 0
7f2c3d3c6000-7f2c3d3db000 r-xp 00000000 08:01 4460113 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2c3d3db000-7f2c3d5da000 ---p 00015000 08:01 4460113 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2c3d5da000-7f2c3d5db000 r--p 00014000 08:01 4460113 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2c3d5db000-7f2c3d5dc000 rw-p 00015000 08:01 4460113 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f2c3d5fb000-7f2c4c000000 r--p 00000000 08:01 4201180 /home/bruno/Documentos/Doutorado/Genomas/M_zebra_v0.assembly.fasta.nsq
7f2c4c000000-7f2c4c021000 rw-p 00000000 00:00 0
7f2c4c021000-7f2c50000000 ---p 00000000 00:00 0
7f2c53685000-7f2c53686000 ---p 00000000 00:00 0
7f2c53686000-7f2c53e86000 rw-p 00000000 00:00 0 [stack:6637]
7f2c54000000-7f2c54021000 rw-p 00000000 00:00 0
7f2c54021000-7f2c58000000 ---p 00000000 00:00 0
7f2c5c000000-7f2c5c021000 rw-p 00000000 00:00 0
7f2c5c021000-7f2c60000000 ---p 00000000 00:00 0
7f2c63e86000-7f2c63e87000 ---p 00000000 00:00 0
7f2c63e87000-7f2c64687000 rw-p 00000000 00:00 0
7f2c64687000-7f2c64688000 ---p 00000000 00:00 0
7f2c64688000-7f2c64e88000 rw-p 00000000 00:00 0 [stack:6633]
7f2c64e88000-7f2c64e89000 ---p 00000000 00:00 0
7f2c64e89000-7f2c65689000 rw-p 00000000 00:00 0 [stack:6632]
7f2c65689000-7f2c65695000 r-xp 00000000 08:01 4456659 /lib/x86_64-linux-gnu/libnss_files-2.15.so
7f2c65695000-7f2c65894000 ---p 0000c000 08:01 4456659 /lib/x86_64-linux-gnu/libnss_files-2.15.so
7f2c65894000-7f2c65895000 r--p 0000b000 08:01 4456659 /lib/x86_64-linux-gnu/libnss_files-2.15.so
7f2c65895000-7f2c65896000 rw-p 0000c000 08:01 4456659 /lib/x86_64-linux-gnu/libnss_files-2.15.so
7f2c65896000-7f2c658a0000 r-xp 00000000 08:01 4456655 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
7f2c658a0000-7f2c65aa0000 ---p 0000a000 08:01 4456655 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
7f2c65aa0000-7f2c65aa1000 r--p 0000a000 08:01 4456655 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
7f2c65aa1000-7f2c65aa2000 rw-p 0000b000 08:01 4456655 /lib/x86_64-linux-gnu/libnss_nis-2.15.so
7f2c65aa2000-7f2c65ab9000 r-xp 00000000 08:01 4456669 /lib/x86_64-linux-gnu/libnsl-2.15.so
7f2c65ab9000-7f2c65cb8000 ---p 00017000 08:01 4456669 /lib/x86_64-linux-gnu/libnsl-2.15.so
7f2c65cb8000-7f2c65cb9000 r--p 00016000 08:01 4456669 /lib/x86_64-linux-gnu/libnsl-2.15.so
7f2c65cb9000-7f2c65cba000 rw-p 00017000 08:01 4456669 /lib/x86_64-linux-gnu/libnsl-2.15.so
7f2c65cba000-7f2c65cbc000 rw-p 00000000 00:00 0
7f2c65cbc000-7f2c65cc4000 r-xp 00000000 08:01 4456673 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
7f2c65cc4000-7f2c65ec3000 ---p 00008000 08:01 4456673 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
7f2c65ec3000-7f2c65ec4000 r--p 00007000 08:01 4456673 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
7f2c65ec4000-7f2c65ec5000 rw-p 00008000 08:01 4456673 /lib/x86_64-linux-gnu/libnss_compat-2.15.so
7f2c65ec5000-7f2c65ed8000 r-xp 00000000 08:01 21764186 /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7f2c65ed8000-7f2c660d7000 ---p 00013000 08:01 21764186 /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7f2c660d7000-7f2c660d8000 r--p 00012000 08:01 21764186 /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7f2c660d8000-7f2c660d9000 rw-p 00013000 08:01 21764186 /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6.1.20120620
7f2c660d9000-7f2c661d4000 r-xp 00000000 08:01 4456670 /lib/x86_64-linux-gnu/libm-2.15.so
7f2c661d4000-7f2c663d3000 ---p 000fb000 08:01 4456670 /lib/x86_64-linux-gnu/libm-2.15.so
7f2c663d3000-7f2c663d4000 r--p 000fa000 08:01 4456670 /lib/x86_64-linux-gnu/libm-2.15.so
7f2c663d4000-7f2c663d5000 rw-p 000fb000 08:01 4456670 /lib/x86_64-linux-gnu/libm-2.15.so
7f2c663d5000-7f2c6658a000 r-xp 00000000 08:01 4456674 /lib/x86_64-linux-gnu/libc-2.15.so
7f2c6658a000-7f2c6678a000 ---p 001b5000 08:01 4456674 /lib/x86_64-linux-gnu/libc-2.15.so
7f2c6678a000-7f2c6678e000 r--p 001b5000 08:01 4456674 /lib/x86_64-linux-gnu/libc-2.15.so
7f2c6678e000-7f2c66790000 rw-p 001b9000 08:01 4456674 /lib/x86_64-linux-gnu/libc-2.15.so
7f2c66790000-7f2c66795000 rw-p 00000000 00:00 0
7f2c66795000-7f2c667ad000 r-xp 00000000 08:01 4456657 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f2c667ad000-7f2c669ac000 ---p 00018000 08:01 4456657 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f2c669ac000-7f2c669ad000 r--p 00017000 08:01 4456657 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f2c669ad000-7f2c669ae000 rw-p 00018000 08:01 4456657 /lib/x86_64-linux-gnu/libpthread-2.15.so
7f2c669ae000-7f2c669b3000 rw-p 00000000 00:00 0
7f2c669b3000-7f2c66a52000 r-xp 00000000 08:01 21764214 /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7f2c66a52000-7f2c66c51000 ---p 0009f000 08:01 21764214 /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7f2c66c51000-7f2c66c54000 r--p 0009e000 08:01 21764214 /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7f2c66c54000-7f2c66c55000 rw-p 000a1000 08:01 21764214 /usr/lib/x86_64-linux-gnu/libncbi.so.6.1.20120620
7f2c66c55000-7f2c66c69000 rw-p 00000000 00:00 0
7f2c66c69000-7f2c67269000 r-xp 00000000 08:01 21764164 /usr/lib/x86_64-linux-gnu/libncbiobj.so.6.1.20120620Abortado (imagem do núcleo gravada)


Thank you very much!
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Old 12-10-2013, 04:37 AM   #2
sphil
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Location: Stuttgart, Germany

Join Date: Apr 2010
Posts: 192
Default

FWIW: have you tried reinstalling the blast suite? Because what is says is:
That your C library thinks you did a double free (that is, you freed (unallocated memory) the same thing twice, which is of course a bug) or that you corrupted its data structures, such as by writing beyond the end of a buffer you allocated.
Since you downloaded it the file might be corrupt or there is bug in freeing in the blast2 suite. try reinstall if this still occurs shoot a mail to the devel-team.
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Old 12-11-2013, 06:44 AM   #3
bfantinatti
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Location: Sao Paulo/Brazil

Join Date: Aug 2012
Posts: 22
Default Yes

Yes, I reinstalled and reformated the database several times.
Using the nt database downloaded from ncbi, it works perfectly. Formating my own database based on a genome I have, if worked perfectly too, but just in the first time. This is the strangest thing: It worked once before.

I installed the blast2 from repositories.
I have a genome in *.fasta.

The database was formated with this command:
formatdb -p F -i My_genome.fasta

Was generated the files My_genome.fasta.nhr, .nin and .nsq.
The analysis was run with this command:
blast2 -p blastn -i MY_FILE.fq -d My_genome.fasta -o MY_FILE.blast.out -a 32
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Old 12-12-2013, 04:42 AM   #4
sphil
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Default

i have installed blast2.2.28+ there you need to use the 'makeblastdb' script to generate a new blast database. Actually there is no formatdb script. There is one named 'blast_formatter' which is to reformat a given onine blast output. Try generating your db with 'makeblastdb'.
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Old 05-13-2014, 11:11 PM   #5
A_Morozov
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Location: Russia, Irkutsk

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Posts: 40
Default

The same bug with Blast 2.2.26 on Linux Mint 15.
Just in case someone still encounters it, it seems to occur only with multiple processors (ie -a >=2), so you can avoid it at the price of longer comparison.
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