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Le 10/13/11 4:21 PM, Luca Capello a écrit : > forwarded 644962 [email protected] > 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 provide the sequence, which comes from unpublished data (and FWIW I am 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 <[email protected]> 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 [email protected]. > > 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@gismo:/srv# export | grep EXCEPTION_STACK_TRACE_LEVEL > (sid)root@gismo:/srv# export EXCEPTION_STACK_TRACE_LEVEL=Debug > (sid)root@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@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@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@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@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@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@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/ iQIcBAEBCAAGBQJOlvr1AAoJEHjcaNsybYQ4M80P/3RdYR2DFlXxH1B8EQYydRVw sEwij2DBYquOEiEsJTiqyiB2XA1ZhTIa5SXhPJ95o5vd4N+EYcyrZmOhS8TbYC6k vB9Ij/IbqNPePDFuqdBT1yqKsCb4B71S6RtluHZbF3tZVk6Y5XFmWOToHZB0JXt/ FyhRbKxwcKRQ7TLk/D7cNV4NAPXYKUxTyXX6ar4KUTMnLC8y1yVAeRocu0YjKhI3 tSPPA4bCugf8Hui0My03cCQnnKMLinDtM3qHkhDN5//uJ2pP+edf5BgJgdnmLZMg awRpQxF6+wDIDpGx7DvSASCYj+Vr+W6YreByO3+sEJxKhcMrpN7Y90Y7BeiortBO PczMRhNF1LlE0segqNel0Dl90mZmsM+jTxNHhtWbQe44dV3ZP4iU2G19bqXcxYTJ +G9PQCEaMyxeZgKm2K/vOdDFakJRt6SyI1j8lYZCPWcqmcXw3cLCfKDy1yoYrhGz /u8cZ6ZqWZzNL41F+bKSoqxNvuEfKSqT7jkkD13vtXjm8Q4A70a4fDFBclDO1shW OmEHaDtb3SjfKqzJYTe3oWQkU6JTnEriCp5wcWBQUFcDGVo0df3h/GwBLVUrebEY grX7beupdQ/4/YclrypJmt/khauHdT+iwHLSyetl2vaQf77WR3cScOLg3p6BzTKZ fo7RChXywA4TZ37zjDQR =foJy -----END PGP SIGNATURE----- -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". 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