FASTA program discussion list

[Jason Stajich <>]

Bill - 

I wanted to report a bug.

I am getting crashes with these errors when I run tfastx36 36.3.5a - I have 
tried with both sse and nonsse compiled versions. 

# /usr/local/src/fasta-36.3.5a/bin/tfastx36 pep genome
TFASTX compares a protein to a translated DNA data bank
 version 36.3.5a Jun, 2011(preload8)
Please cite:
 Pearson et al, Genomics (1997) 46:24-36

Query: pep
  1>>>YPL160W  Chr 16   - 1091 aa
Library: genome
  160439179 residues in 38098 sequences

Statistics: Altschul/Gish params: n0: 1091 Lambda: 0.188 K: 0.034 H: 0.170
 statistics sampled from 2324 (2329) to 2324 sequences
Algorithm: TFASTX (3.7 Nov 2010) [optimized]
Parameters: BL50 matrix (15:-5), open/ext: -12/-2, shift: -20
 ktup: 2, E-join: 0.5 (0.202), E-opt: 0.1 (0.031), width:  16
 Scan time: 26.750

The best scores are:                             initn opt bits E(38258)
NODE_40475_length_1214_cov_115.716637 (1280) [f] 1549  985 272.2 6.1e-72
NODE_40474_length_487_cov_116.889114  ( 553) [f]  559  524 147.2 1.1e-34
NODE_40473_length_5132_cov_30.160561  (5198) [f] 1229  524 147.1 1.1e-33
NODE_261821_length_79851_cov_31.02583 (79917) [f]  657  530 148.8 5.6e-33
NODE_40477_length_1116_cov_116.573479 (1182) [f]  432  320 91.8 1.1e-17

*** glibc detected *** /usr/local/src/fasta-36.3.5a/bin/tfastx36: double free 
or corruption (out): 0x00002aaaac075d70 ***
======= Backtrace: =========
/lib64/libc.so.6[0x374ac7245f]
/lib64/libc.so.6(cfree+0x4b)[0x374ac728bb]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x41c6be]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x41daf6]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x41dc63]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x41e18c]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x40ebde]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x4089f3]
/usr/local/src/fasta-36.3.5a/bin/tfastx36[0x406ea7]
/lib64/libpthread.so.0[0x374b80673d]
/lib64/libc.so.6(clone+0x6d)[0x374acd44bd]
======= Memory map: ========
00400000-0043f000 r-xp 00000000 08:03 107053731                          
/usr/local/src/fasta-36.3.5a/bin/tfastx36
0063e000-00649000 rw-p 0003e000 08:03 107053731                          
/usr/local/src/fasta-36.3.5a/bin/tfastx36


uname -a
Linux puffball 2.6.18-238.12.1.el5 #1 SMP Tue May 31 13:22:04 EDT 2011 x86_64 
x86_64 x86_64 GNU/Linux


Thanks,
Jason
-- 
Jason E Stajich, PhD
Assistant Professor, Plant Pathology & Microbiology
Institute for Integrative Genome Biology
University of California, Riverside
951.827.2363
http://lab.stajich.org http://fungalgenomes.org http://fungidb.org ;
twitter: @stajichlab @hyphaltip @fungalgenomes @fungidb
http://planpathology.ucr.edu http://genomics.ucr.edu