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

[Luca Capello]

Hi there!

On Thu, 13 Oct 2011 17:41:52 +0200, Aaron M. Ucko wrote:
> Luca Capello <luca at pca.it> writes:
>
>> (sid)root at gismo:/srv# export EXCEPTION_STACK_TRACE_LEVEL=Debug
>
> Please excuse my brain fault and try again with
> EXCEPTION_STACK_TRACE_LEVEL=Error .

No problem, here we are, but nothing changed:
=====
(sid)root at gismo:/srv# export | grep EXCEPTION_STACK_TRACE_LEVEL
(sid)root at gismo:/srv# export EXCEPTION_STACK_TRACE_LEVEL=Error
(sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
 -db /srv/blastDB/swissprot -out [SEQUENCE-8].asn1.num-threads-1.error \
 -evalue 0.001 -num_threads 1 -outfmt 11
Warning: (802.8)  NULL pointer found in container: skipping
Warning: (802.8)  NULL pointer found in container: skipping

real    5m21.096s
user    0m5.788s
sys     0m2.184s

(sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
 -db /srv/blastDB/swissprot -out [SEQUENCE-8].xml.num-threads-1.error \
 -evalue 0.001 -num_threads 1 -outfmt 5
Error: NCBI C++ Exception:
    "/home/osallou/DEBIAN-MED/trunk/packages/ncbi-blast+/build-area/ncbi-blast+-2.2.25/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.


real    4m57.328s
user    0m5.816s
sys     0m1.980s

(sid)root at gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
 -db /srv/blastDB/swissprot -out [SEQUENCE-8].no-outfmt.num-threads-1.error \
 -evalue 0.001 -num_threads 1
Error: NCBI C++ Exception:
    "/home/osallou/DEBIAN-MED/trunk/packages/ncbi-blast+/build-area/ncbi-blast+-2.2.25/c++/src/corelib/ncbiobj.cpp", line 689: Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.


real    5m5.023s
user    0m5.764s
sys     0m1.956s

(sid)root at gismo:/srv# ls -l [SEQUENCE-8].*
-rw-r--r-- 1 4294967294 4294967294 205480 Oct  6 07:04 [SEQUENCE-8].asn1.num-threads-1
-rw-r--r-- 1 4294967294 4294967294      0 Oct 13 11:55 [SEQUENCE-8].asn1.num-threads-1.debug
-rw-r--r-- 1 4294967294 4294967294 205480 Oct 14 10:42 [SEQUENCE-8].asn1.num-threads-1.error
-rw-r--r-- 1       1000 adm           242 Oct  6 06:59 [SEQUENCE-8].fasta
-rw-r--r-- 1 4294967294 4294967294    774 Oct  6 07:49 [SEQUENCE-8].no-outfmt.num-threads-1
-rw-r--r-- 1 4294967294 4294967294      0 Oct 13 11:58 [SEQUENCE-8].no-outfmt.num-threads-1.debug
-rw-r--r-- 1 4294967294 4294967294    774 Oct 14 10:59 [SEQUENCE-8].no-outfmt.num-threads-1.error
-rw-r--r-- 1 4294967294 4294967294      0 Oct  6 07:06 [SEQUENCE-8].xml.num-threads-1
-rw-r--r-- 1 4294967294 4294967294      0 Oct 13 11:55 [SEQUENCE-8].xml.num-threads-1.debug
-rw-r--r-- 1 4294967294 4294967294      0 Oct 14 10:47 [SEQUENCE-8].xml.num-threads-1.error

(sid)root at gismo:/srv#
=====

The output of [SEQUENCE-8].no-outfmt.num-threads-1.error is the same as
[SEQUENCE-8].no-outfmt.num-threads-1 at:

  <http://bugs.debian.org/cgi-bin/bugreport.cgi?archive=yes&bug=644962#5>

I am sending the sequence to the BLAST folks at NCBI.

Thx, bye,
Gismo / Luca
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