Bug#644962: ncbi-blast+: [blastp] Critical: ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL pointer.

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

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.



filename=ncbi-blast+_2.2.25-6_blastp_NULL-pointer.log.gz

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