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
Description: Binary data
pgpMXBS3tvNXH.pgp
Description: PGP signature
