Hi there! On Thu, 13 Oct 2011 17:41:52 +0200, Aaron M. Ucko wrote: > Luca Capello <l...@pca.it> writes: > >> (sid)root@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@gismo:/srv# export | grep EXCEPTION_STACK_TRACE_LEVEL
(sid)root@gismo:/srv# export EXCEPTION_STACK_TRACE_LEVEL=Error
(sid)root@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@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@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@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@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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