[Debian-med-packaging] Bug#644962: cannot reproduce

[Olivier Sallou]

-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256



Le 10/13/11 4:21 PM, Luca Capello a écrit :
> forwarded 644962 blastsoft at ncbi.nlm.nih.gov
> thanks
>
> Hi there!
>
> For the BLAST folks at NCBI, please see <http://bugs.debian.org/644962>.
>
> On Tue, 11 Oct 2011 13:37:39 +0200, Olivier Sallou wrote:
>> I unfortunatly cannot reproduce the problem. I would need the sequence
>> that creates the issue, or a fake one reproducing the error.
>> Could be a sequence format that raise an error (bad characters?, even if
>> I tried to do so also).
>
> Just to repeat myself: the sequence does not seem strange at all and the
> fact that the BLAST website does not give any error means that it should
> work. FYI, BioEdit (through WINE) opens it without any problem:
>
> <http://www.mbio.ncsu.edu/BioEdit/bioedit.html>
>
>> If sending the sequence is only an issue with the fact it is logged on
>> public server, maybe you could send me the sequence directly.
>
> Given that the upstream BLAST authors asked to be directly contacted, do
> you still want to try to debug this?

I will indeed let upstream have a look and will follow the issue.

> As I wrote, I can *privately*
> provide the sequence, which comes from unpublished data (and FWIW I am
> not working on these data).

>
>
> On Tue, 11 Oct 2011 17:57:54 +0200, Aaron M. Ucko wrote:
>> On Tue, 11 Oct 2011 16:30:01 +0200, Aaron M. Ucko wrote:
>>> Luca Capello <luca at pca.it> writes:
>>>> [3] RID 8UUGT24C013, in case someone will have access to the logs
>>>
>>> I don't have access, but will forward this report to coworkers who do.
>>
>> They report that the details already expired from their records, but
>> invite you to contact them directly at blastsoft at ncbi.nlm.nih.gov.
>
> Done with this email, forward set as well.
>
>> FWIW, they're also preparing to issue a 2.2.26+ release that could
>> potentially fare better on your query.
>
> I can easily use the machine with Mac OS X 10.6.8 to test this new
> release if needed: all the necessary software to build BLAST+ is already
> installed there. Should any pre-release be tested, feel free to provide
> a link to the tarball or a VCS repository.
>
>>>> Warning: (802.8) NULL pointer found in container: skipping
>>>
>>> It looks like you're somehow getting NULL results mixed in; raw ASN.1
>>> output elides them, but other formats entail further processing that
>>> doesn't allow for that possibility (which shouldn't happen, to be fair).
>>> It's hard to tell exactly why, particularly without access to your query
>>> data (whose confidentiality I understand); however, repeating the failing
>>> commands with the environment setting EXCEPTION_STACK_TRACE_LEVEL=Debug
>>> may shed some light on the matter. Could you please do so?
>
> Even worse ;-)
> =====
> (sid)root at gismo:/srv# export | grep EXCEPTION_STACK_TRACE_LEVEL
> (sid)root at gismo:/srv# export EXCEPTION_STACK_TRACE_LEVEL=Debug
> (sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
> -db /srv/blastDB/swissprot -out [SEQUENCE-8].asn1.num-threads-1.debug \
> -evalue 0.001 -num_threads 1 -outfmt 11
> Segmentation fault
>
> real 0m1.796s
> user 0m0.168s
> sys 0m0.240s
>
> (sid)root at gismo:/srv# dmesg | tail -n 1
> [17411.690415] blastp[31722]: segfault at 7fff9f272ff8 ip
00007fd1e8839378 \
> sp 00007fff9f273000 error 6 in libstdc++.so.6.0.16[7fd1e8780000+e5000]
>
> (sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
> -db /srv/blastDB/swissprot -out [SEQUENCE-8].xml.num-threads-1.debug \
> -evalue 0.001 -num_threads 1 -outfmt 5
> Segmentation fault
>
> real 0m0.479s
> user 0m0.172s
> sys 0m0.200s
>
> (sid)root at gismo:/srv# dmesg | tail -n 1
> [17448.907143] blastp[31852]: segfault at 7fff8b36dff8 ip
00007f34bd5d34b0 \
> sp 00007fff8b36e028 error 6 in libstdc++.so.6.0.16[7f34bd531000+e5000]
>
> (sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
> -db /srv/blastDB/swissprot -out
[SEQUENCE-8].no-outfmt.num-threads-1.debug \
> -evalue 0.001 -num_threads 1
> Segmentation fault
>
> real 0m0.501s
> user 0m0.160s
> sys 0m0.220s
>
> (sid)root at gismo:/srv# dmesg | tail -n 1
> [17471.719104] blastp[31924]: segfault at 7fff6f04fff8 ip
00007f914aa7abd6 \
> sp 00007fff6f050000 error 6 in libc-2.13.so[7f914aa06000+17a000]
>
> (sid)root at gismo:/srv#
> =====
>
> Thx, bye,
> Gismo / Luca

- -- 
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95

gpg key id: 4096R/326D8438  (pgp.mit.edu)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335  D26D 78DC 68DB 326D 8438

-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (Darwin)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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=foJy
-----END PGP SIGNATURE-----