Your message dated Mon, 17 Oct 2011 21:43:55 +0200
with message-id <[email protected]>
and subject line Re: [blastsoft] cannot reproduce
has caused the Debian Bug report #644962,
regarding ncbi-blast+: [blastp] Critical:
ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.
to be marked as done.
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--
644962: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=644962
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: ncbi-blast+
Version: 2.2.25-6
Severity: important
File: /usr/bin/blastp
Tags: upstream
Usertags: unige.ch-jmlab
Hi there!
This error is reproducible on a Mac OS X 10.6.8 with manually-compiled
2.2.24+ and 2.2.25+, on a Debian lenny 5.0.8 with manually-compiled
2.2.24+ and on a Debian sid chroot on my laptop [1] with the stock
Debian ncbi-blast+ package (version 2.2.25-6). However, this does not
happen with the online NCBI BLAST interface [2][3].
[1] <http://bugs.debian.org/600671>
[2] <http://blast.ncbi.nlm.nih.gov/Blast.cgi>
[3] RID 8UUGT24C013, in case someone will have access to the logs
Full outputs are attached: I tried to hunt down the problem and finally
I was able to restrict it to a single sequence (which does not seems
"strange" at all). This sequence is unfortunately not attached to this
bug report for privacy reasons.
=====
(sid)root@gismo:/srv# grep -c "^>" 775.fasta
776
(sid)root@gismo:/srv# time blastp -query 775.fasta \
-db /srv/blastDB/swissprot -out 775.xml.num-threads-1 \
-evalue 0.001 -num_threads 1 -outfmt 5
Selenocysteine (U) at position 47 replaced by X
[similar output repeated]
Selenocysteine (U) at position 273 replaced by X
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 325m9.295s
user 93m38.911s
sys 1m32.106s
(sid)root@gismo:/srv# time blastp -query 775.fasta \
-db /srv/blastDB/swissprot -out 775.no-outfmt.num-threads-1 \
-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 9m19.836s
user 2m6.664s
sys 0m2.712s
(sid)root@gismo:/srv# time blastp -query 775.fasta \
-db /srv/blastDB/swissprot -out 775.asn1.num-threads-1 \
-evalue 0.001 -num_threads 1 -outfmt 11
Warning: (802.8) NULL pointer found in container: skipping
[similar output repeated]
Warning: (802.8) NULL pointer found in container: skipping
Selenocysteine (U) at position 47 replaced by X
[similar output repeated]
Selenocysteine (U) at position 47 replaced by X
[...]
Selenocysteine (U) at position 273 replaced by X
Warning: (802.8) NULL pointer found in container: skipping
real 314m51.481s
user 95m31.202s
sys 1m34.290s
(sid)root@gismo:/srv# ls -l
total 162292
-rw-r--r-- 1 4294967294 4294967294 164438156 Oct 5 19:12
775.asn1.num-threads-1
-rw-r--r-- 1 4294967294 4294967294 405219 Oct 4 16:51 775.fasta
-rw-r--r-- 1 1002 adm 172 Oct 4 16:52 775.fasta.cmd
-rw-r--r-- 1 4294967294 4294967294 1291436 Oct 5 13:49
775.no-outfmt.num-threads-1
-rw-r--r-- 1 4294967294 4294967294 0 Oct 5 07:44
775.xml.num-threads-1
drwxrwxr-x 939 501 dialout 31926 Oct 4 22:06 blastDB
(sid)root@gismo:/srv#
=====
ASN.1 output is OK [5], but not standard and XML outputs, but wait, when
using the standard output something is written.
[5] unfortunately, I deleted the asn1 file above.
=====
(sid)root@gismo:/srv# grep "Query= " 775.no-outfmt.num-threads-1
Query= [SEQUENCE-1]
Query= [SEQUENCE-2]
Query= [SEQUENCE-3]
Query= [SEQUENCE-4]
Query= [SEQUENCE-5]
Query= [SEQUENCE-6]
Query= [SEQUENCE-7]
Query= [SEQUENCE-8]
(sid)root@gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
-db /srv/blastDB/swissprot -out [SEQUENCE-8].asn1.num-threads-1 \
-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 4m47.073s
user 0m4.988s
sys 0m1.840s
(sid)root@gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
-db /srv/blastDB/swissprot -out [SEQUENCE-8].xml.num-threads-1 \
-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 4m35.507s
user 0m4.864s
sys 0m1.884s
(sid)root@gismo:/srv# time blastp -query [SEQUENCE-8].fasta \
-db /srv/blastDB/swissprot -out [SEQUENCE-8].no-outfmt.num-threads-1 \
-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 4m39.969s
user 0m5.072s
sys 0m1.688s
(sid)root@gismo:/srv# ls -l
total 1916
-rw-r--r-- 1 4294967294 4294967294 164438156 Oct 5 19:12
775.asn1.num-threads-1
-rw-r--r-- 1 4294967294 4294967294 405219 Oct 4 16:51 775.fasta
-rw-r--r-- 1 1002 adm 172 Oct 4 16:52 775.fasta.cmd
-rw-r--r-- 1 4294967294 4294967294 1291436 Oct 5 13:49
775.no-outfmt.num-threads-1
-rw-r--r-- 1 4294967294 4294967294 0 Oct 5 07:44
775.xml.num-threads-1
drwxrwxr-x 939 501 dialout 31926 Oct 4 22:06 blastDB
-rw-r--r-- 1 4294967294 4294967294 205480 Oct 6 07:04
[SEQUENCE-8].asn1.num-threads-1
-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 6 07:06
[SEQUENCE-8].xml.num-threads-1
(sid)root@gismo:/srv# cat [SEQUENCE-8].no-outfmt.num-threads-1
BLASTP 2.2.25+
Reference: Stephen F. Altschul, Thomas L. Madden, Alejandro A.
Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J.
Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of
protein database search programs", Nucleic Acids Res. 25:3389-3402.
Reference for composition-based statistics: Alejandro A. Schaffer,
L. Aravind, Thomas L. Madden, Sergei Shavirin, John L. Spouge, Yuri
I. Wolf, Eugene V. Koonin, and Stephen F. Altschul (2001),
"Improving the accuracy of PSI-BLAST protein database searches with
composition-based statistics and other refinements", Nucleic Acids
Res. 29:2994-3005.
Database: Non-redundant SwissProt sequences
447,625 sequences; 166,764,588 total letters
Query= [SEQUENCE-8]
Length=215
(sid)root@gismo:/srv#
=====
Thx, bye,
Gismo / Luca
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.1.0-rc7-amd64 (SMP w/2 CPU cores)
Locale: LANG=C, LC_CTYPE=C (charmap=ANSI_X3.4-1968) (ignored: LC_ALL set to C)
Shell: /bin/sh linked to /bin/dash
Versions of packages ncbi-blast+ depends on:
ii libbz2-1.0 1.0.5-7
ii libc6 2.13-21
ii libgcc1 1:4.6.1-13
ii libpcre3 8.12-4
ii libstdc++6 4.6.1-13
ii ncbi-data 6.1.20110713-2
ii perl 5.12.4-5
ii python 2.7.2-7
ii zlib1g 1:1.2.3.4.dfsg-3
ncbi-blast+ recommends no packages.
ncbi-blast+ suggests no packages.
-- no debconf information
ncbi-blast+_2.2.25-6_blastp_NULL-pointer.log.gz
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--- End Message ---
--- Begin Message ---
Version: 2.2.25-6
Hi there!
On Fri, 14 Oct 2011 21:50:08 +0200, Madden, Tom (NIH/NLM/NCBI) [E] wrote:
> I've tried a number of runs with your query and the blastp binaries for
> 2.2.24 and 2.2.25 both under CentOS and MacOSX (10.6.8). I have not seen
> a problem with any of those. I also tried valgrind on the CentOS machine.
> Some of the runs that I did on a mac are below. I've been using a
> swissprot that I built from the FASTA files on the NCBI FTP site. One
> possibility is that your swissprot database is different than mine, and
> the results are different enough that our formatter trips over a problem
> when it formats them.
It was indeed a problem with the databases, which BTW are the one you
can download with BLAST+ update_blastdb. I downloaded a new copy of the
two needed databases (which means not only swissprot, but also nr) and
everything worked.
However, the problem was not swissprot, but actually nr. The MacOSX
machine where the databases reside automatically update them every night
and I found two Perl errors (which I will not investigate further):
Downloading nr.01.tar.gz... Unable to close datastream at
/usr/local/bin/update_blastdb.pl line 181
Downloading nr.00.tar.gz... Timeout at /System/Library/Perl/5.10.0/Net/FTP.pm
line 491
I am sorry for the noise, I did not re-download the databases assuming
that everything was fine from that side, also because other users of the
same pool did not report any error, my fault.
Thx, bye,
Gismo / Luca
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