invalid pointer - Githubissues

What steps will reproduce the problem?
1. Install idba according to instructions in README file
2. Try to run it on a single-reads 454 file:

bin/idba -r 
~/Project_II/CBAY_seqs/454/fasta_newbler-trimmed/newbler-trimmed_G7173.x.fasta 
-o test_assembly_newbler-trimmed_G7173 

What is the expected output? What do you see instead?
Assembly is expected. Instead, I get this:
*** glibc detected *** bin/idba: munmap_chunk(): invalid pointer: 
0x00000000014d0110 ***
======= Backtrace: =========
/lib64/libc.so.6[0x324f8751e6]
bin/idba[0x45648b]
bin/idba[0x456a4a]
bin/idba[0x4550fd]
bin/idba[0x41207c]
bin/idba[0x412937]
bin/idba[0x407b33]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x324f81ec5d]
bin/idba[0x403539]
======= Memory map: ========
00400000-00468000 r-xp 00000000 fd:01 65931198                           
/home/khaleel/assemblers/idba-0.19/bin/idba
00667000-00669000 rw-p 00067000 fd:01 65931198                           
/home/khaleel/assemblers/idba-0.19/bin/idba
00669000-00869000 rw-p 00000000 00:00 0 
014ca000-014eb000 rw-p 00000000 00:00 0                                  [heap]
324f400000-324f41e000 r-xp 00000000 fd:00 9437186                        
/lib64/ld-2.12.2.so
324f61d000-324f61e000 r--p 0001d000 fd:00 9437186                        
/lib64/ld-2.12.2.so
324f61e000-324f61f000 rw-p 0001e000 fd:00 9437186                        
/lib64/ld-2.12.2.so
324f61f000-324f620000 rw-p 00000000 00:00 0 
324f800000-324f974000 r-xp 00000000 fd:00 9437190                        
/lib64/libc-2.12.2.so
324f974000-324fb74000 ---p 00174000 fd:00 9437190                        
/lib64/libc-2.12.2.so
324fb74000-324fb78000 r--p 00174000 fd:00 9437190                        
/lib64/libc-2.12.2.so
324fb78000-324fb79000 rw-p 00178000 fd:00 9437190                        
/lib64/libc-2.12.2.so
324fb79000-324fb7e000 rw-p 00000000 00:00 0 
324fc00000-324fc83000 r-xp 00000000 fd:00 9437202                        
/lib64/libm-2.12.2.so
324fc83000-324fe82000 ---p 00083000 fd:00 9437202                        
/lib64/libm-2.12.2.so
324fe82000-324fe83000 r--p 00082000 fd:00 9437202                        
/lib64/libm-2.12.2.so
324fe83000-324fe84000 rw-p 00083000 fd:00 9437202                        
/lib64/libm-2.12.2.so
3250400000-3250417000 r-xp 00000000 fd:00 9437195                        
/lib64/libpthread-2.12.2.so
3250417000-3250616000 ---p 00017000 fd:00 9437195                        
/lib64/libpthread-2.12.2.so
3250616000-3250617000 r--p 00016000 fd:00 9437195                        
/lib64/libpthread-2.12.2.so
3250617000-3250618000 rw-p 00017000 fd:00 9437195                        
/lib64/libpthread-2.12.2.so
3250618000-325061c000 rw-p 00000000 00:00 0 
3250c00000-3250c07000 r-xp 00000000 fd:00 9437198                        
/lib64/librt-2.12.2.so
3250c07000-3250e06000 ---p 00007000 fd:00 9437198                        
/lib64/librt-2.12.2.so
3250e06000-3250e07000 r--p 00006000 fd:00 9437198                        
/lib64/librt-2.12.2.so
3250e07000-3250e08000 rw-p 00007000 fd:00 9437198                        
/lib64/librt-2.12.2.so
3251000000-325100d000 r-xp 00000000 fd:00 274921                         
/usr/lib64/libgomp.so.1.0.0
325100d000-325120c000 ---p 0000d000 fd:00 274921                         
/usr/lib64/libgomp.so.1.0.0
325120c000-325120d000 rw-p 0000c000 fd:00 274921                         
/usr/lib64/libgomp.so.1.0.0
3252800000-3252816000 r-xp 00000000 fd:00 9437204                        
/lib64/libgcc_s-4.4.5-20101113.so.1
3252816000-3252a15000 ---p 00016000 fd:00 9437204                        
/lib64/libgcc_s-4.4.5-20101113.so.1
3252a15000-3252a16000 rw-p 00015000 fd:00 9437204                        
/lib64/libgcc_s-4.4.5-20101113.so.1
3254000000-32540e8000 r-xp 00000000 fd:00 271634                         
/usr/lib64/libstdc++.so.6.0.13
32540e8000-32542e8000 ---p 000e8000 fd:00 271634                         
/usr/lib64/libstdc++.so.6.0.13
32542e8000-32542ef000 r--p 000e8000 fd:00 271634                         
/usr/lib64/libstdc++.so.6.0.13
32542ef000-32542f1000 rw-p 000ef000 fd:00 271634                         
/usr/lib64/libstdc++.so.6.0.13
32542f1000-3254306000 rw-p 00000000 00:00 0 
7fa71ceb5000-7fa71da5e000 rw-p 00000000 00:00 0 
7fa71da75000-7fa71da76000 rw-p 00000000 00:00 0 
7fffa7381000-7fffa73a2000 rw-p 00000000 00:00 0                          [stack]
7fffa73ff000-7fffa7400000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  
[vsyscall]
Aborted (core dumped)

What version of the product are you using? On what operating system?
idba-0.19 on Linux 2.6.34.8-68.fc13.x86_64

Please provide any additional information below.

Original issue reported on code.google.com by Sari.Kha...@gmail.com on 8 Aug 2011 at 1:11

I get basically same output/error when attempting to run on single-reads Ion 
Torrent file (installation works on provided example data):

*** glibc detected *** 
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba: 
munmap_chunk(): invalid pointer: 0x0000000000875fa0 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x75018)[0x7f42d8b87018]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
45bb63]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
45c3bd]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
45d892]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
45a942]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
418766]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
419b57]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
406d5c]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f42d8b30bc6]
/home/panfs/cbs/projects/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba[0x
403cb9]
======= Memory map: ========
00400000-0046d000 r-xp 00000000 00:2f 421959633                          
/panfs1/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba
0066c000-0066d000 r--p 0006c000 00:2f 421959633                          
/panfs1/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba
0066d000-0066e000 rw-p 0006d000 00:2f 421959633                          
/panfs1/cge/people/rkmo/Applications/idba_v0.19/bin/metaidba
0066e000-0088f000 rw-p 00000000 00:00 0                                  [heap]
7f42d7d66000-7f42d8909000 rw-p 00000000 00:00 0 
7f42d8909000-7f42d8911000 r-xp 00000000 08:08 17804240                   
/lib64/librt-2.11.1.so
7f42d8911000-7f42d8b10000 ---p 00008000 08:08 17804240                   
/lib64/librt-2.11.1.so
7f42d8b10000-7f42d8b11000 r--p 00007000 08:08 17804240                   
/lib64/librt-2.11.1.so
7f42d8b11000-7f42d8b12000 rw-p 00008000 08:08 17804240                   
/lib64/librt-2.11.1.so
7f42d8b12000-7f42d8c66000 r-xp 00000000 08:08 17804176                   
/lib64/libc-2.11.1.so
7f42d8c66000-7f42d8e66000 ---p 00154000 08:08 17804176                   
/lib64/libc-2.11.1.so
7f42d8e66000-7f42d8e6a000 r--p 00154000 08:08 17804176                   
/lib64/libc-2.11.1.so
7f42d8e6a000-7f42d8e6b000 rw-p 00158000 08:08 17804176                   
/lib64/libc-2.11.1.so
7f42d8e6b000-7f42d8e70000 rw-p 00000000 00:00 0 
7f42d8e70000-7f42d8e87000 r-xp 00000000 08:08 17804237                   
/lib64/libpthread-2.11.1.so
7f42d8e87000-7f42d9087000 ---p 00017000 08:08 17804237                   
/lib64/libpthread-2.11.1.so
7f42d9087000-7f42d9088000 r--p 00017000 08:08 17804237                   
/lib64/libpthread-2.11.1.so
7f42d9088000-7f42d9089000 rw-p 00018000 08:08 17804237                   
/lib64/libpthread-2.11.1.so
7f42d9089000-7f42d908d000 rw-p 00000000 00:00 0 
7f42d908d000-7f42d90a3000 r-xp 00000000 08:08 17804197                   
/lib64/libgcc_s.so.1
7f42d90a3000-7f42d92a2000 ---p 00016000 08:08 17804197                   
/lib64/libgcc_s.so.1
7f42d92a2000-7f42d92a3000 r--p 00015000 08:08 17804197                   
/lib64/libgcc_s.so.1
7f42d92a3000-7f42d92a4000 rw-p 00016000 08:08 17804197                   
/lib64/libgcc_s.so.1
7f42d92a4000-7f42d92ac000 r-xp 00000000 08:08 2511234                    
/usr/lib64/libgomp.so.1.0.0
7f42d92ac000-7f42d94ab000 ---p 00008000 08:08 2511234                    
/usr/lib64/libgomp.so.1.0.0
7f42d94ab000-7f42d94ac000 r--p 00007000 08:08 2511234                    
/usr/lib64/libgomp.so.1.0.0
7f42d94ac000-7f42d94ad000 rw-p 00008000 08:08 2511234                    
/usr/lib64/libgomp.so.1.0.0
7f42d94ad000-7f42d9502000 r-xp 00000000 08:08 17804207                   
/lib64/libm-2.11.1.so
7f42d9502000-7f42d9701000 ---p 00055000 08:08 17804207                   
/lib64/libm-2.11.1.so
7f42d9701000-7f42d9702000 r--p 00054000 08:08 17804207                   
/lib64/libm-2.11.1.so
7f42d9702000-7f42d9703000 rw-p 00055000 08:08 17804207                   
/lib64/libm-2.11.1.so
7f42d9703000-7f42d97f3000 r-xp 00000000 08:08 2511611                    
/usr/lib64/libstdc++.so.6.0.10
7f42d97f3000-7f42d99f2000 ---p 000f0000 08:08 2511611                    
/usr/lib64/libstdc++.so.6.0.10
7f42d99f2000-7f42d99f9000 r--p 000ef000 08:08 2511611                    
/usr/lib64/libstdc++.so.6.0.10
7f42d99f9000-7f42d99fb000 rw-p 000f6000 08:08 2511611                    
/usr/lib64/libstdc++.so.6.0.10
7f42d99fb000-7f42d9a0e000 rw-p 00000000 00:00 0 
7f42d9a0e000-7f42d9a2d000 r-xp 00000000 08:08 17804163                   
/lib64/ld-2.11.1.so
7f42d9bed000-7f42d9bf3000 rw-p 00000000 00:00 0 
7f42d9c2b000-7f42d9c2c000 rw-p 00000000 00:00 0 
7f42d9c2c000-7f42d9c2d000 r--p 0001e000 08:08 17804163                   
/lib64/ld-2.11.1.so
7f42d9c2d000-7f42d9c2e000 rw-p 0001f000 08:08 17804163                   
/lib64/ld-2.11.1.so
7f42d9c2e000-7f42d9c2f000 rw-p 00000000 00:00 0 
7fffa73ee000-7fffa7404000 rw-p 00000000 00:00 0                          [stack]
7fffa7445000-7fffa7446000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  
[vsyscall]
Abort

Original comment by rolk...@gmail.com on 13 Aug 2012 at 9:14

yuhy100 / hku-idba

invalid pointer #2