Question: Error in running blast?
0
gravatar for majeedaasim
7 months ago by
majeedaasim20
United States
majeedaasim20 wrote:

I ran blastall through proteinortho but it gives me the following error:

**Step 2**
Running blast analysis: 0% (0/10)*** Error in `blastall': double free or corruption (fasttop): 0x00007fa53c020160 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7fa5556407e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7fa55564937a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7fa55564d53c]
/usr/lib/x86_64-linux-gnu/libncbi.so.6(Nlm_ReleaseAppContext+0x87)[0x7fa555bceb17]
blastall(NlmThreadExit+0x73)[0x55bbece786c3]
blastall(+0xa787)[0x55bbece78787]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x7fa55599a6ba]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fa5556d041

Aborted (core dumped)
Segmentation fault (core dumped)
*** Error in `blastall': corrupted size vs. prev_size: 0x000055c1b6b99440 ***
======= Backtrace: =========
blast • 589 views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 7 months ago by majeedaasim20
2

any particular reason you're still using blastall in stead of blast+ implementation? what is the exact command you're trying to run? Looks like you might have issues running it on multiple cores

ADD REPLYlink written 7 months ago by lieven.sterck2.2k

Yes actually there appears segmentation error. I am using proteinortho version 5 to find gene orthology. THe programme uses reciprocal blastall.

ADD REPLYlink written 7 months ago by majeedaasim20

This looks like a bug. This type of error usually happens when the program tries to use memory that it wasn't allocated. This should be reported to the software authors. However, since blastall is deprecated, you should probably notify the authors of proteinortho.

ADD REPLYlink written 7 months ago by Jean-Karim Heriche16k

Seems like a bug in the program. The error means that the program is trying to double free the memory, which was already free in the first place (or probably it corrupted the data-structure to which it was writing).

what was your actual command line?

ADD REPLYlink written 7 months ago by Santosh Anand3.9k

The command I used is

proteinortho5.pl fasta1 fasta 2 fasta3 fasta4 fasta5 fasta 6 -p=blastn -clean
ADD REPLYlink modified 6 months ago by Ram17k • written 7 months ago by majeedaasim20
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