minialign: error in minialign

Hello,

I am trying to align some Pacbio reads using this command, after having built the index:

minialign -l ref_index.mai SubPacbio.fq > out.sam

This returns

*** Error in `minialign': double free or corruption (out): 0x0000000045466280 ***
======= Backtrace: =========
/usr/lib/libc.so.6(+0x722ab)[0x7fbd942cf2ab]
/usr/lib/libc.so.6(+0x7890e)[0x7fbd942d590e]
/usr/lib/libc.so.6(+0x7911e)[0x7fbd942d611e]
minialign[0x416547]
minialign[0x402028]
/usr/lib/libc.so.6(__libc_start_main+0xf1)[0x7fbd9427d511]
minialign[0x40475a]
======= Memory map: ========
00400000-00463000 r-xp 00000000 08:13 1183949                            /usr/local/bin/minialign
00662000-00663000 r--p 00062000 08:13 1183949                            /usr/local/bin/minialign
00663000-00664000 rw-p 00063000 08:13 1183949                            /usr/local/bin/minialign
00664000-00666000 rw-p 00000000 00:00 0 
014d7000-455ba000 rw-p 00000000 00:00 0                                  [heap]
7fbd84000000-7fbd84021000 rw-p 00000000 00:00 0 
7fbd84021000-7fbd88000000 ---p 00000000 00:00 0 
7fbd885f2000-7fbd88608000 r-xp 00000000 08:13 791916                     /usr/lib/libgcc_s.so.1
7fbd88608000-7fbd88807000 ---p 00016000 08:13 791916                     /usr/lib/libgcc_s.so.1
7fbd88807000-7fbd88808000 r--p 00015000 08:13 791916                     /usr/lib/libgcc_s.so.1
7fbd88808000-7fbd88809000 rw-p 00016000 08:13 791916                     /usr/lib/libgcc_s.so.1
7fbd88809000-7fbd9425d000 rw-p 00000000 00:00 0 
7fbd9425d000-7fbd943f8000 r-xp 00000000 08:13 791851                     /usr/lib/libc-2.25.so
7fbd943f8000-7fbd945f7000 ---p 0019b000 08:13 791851                     /usr/lib/libc-2.25.so
7fbd945f7000-7fbd945fb000 r--p 0019a000 08:13 791851                     /usr/lib/libc-2.25.so
7fbd945fb000-7fbd945fd000 rw-p 0019e000 08:13 791851                     /usr/lib/libc-2.25.so
7fbd945fd000-7fbd94601000 rw-p 00000000 00:00 0 
7fbd94601000-7fbd9461a000 r-xp 00000000 08:13 792063                     /usr/lib/libpthread-2.25.so
7fbd9461a000-7fbd94819000 ---p 00019000 08:13 792063                     /usr/lib/libpthread-2.25.so
7fbd94819000-7fbd9481a000 r--p 00018000 08:13 792063                     /usr/lib/libpthread-2.25.so
7fbd9481a000-7fbd9481b000 rw-p 00019000 08:13 792063                     /usr/lib/libpthread-2.25.so
7fbd9481b000-7fbd9481f000 rw-p 00000000 00:00 0 
7fbd9481f000-7fbd94835000 r-xp 00000000 08:13 792142                     /usr/lib/libz.so.1.2.11
7fbd94835000-7fbd94a34000 ---p 00016000 08:13 792142                     /usr/lib/libz.so.1.2.11
7fbd94a34000-7fbd94a35000 r--p 00015000 08:13 792142                     /usr/lib/libz.so.1.2.11
7fbd94a35000-7fbd94a36000 rw-p 00016000 08:13 792142                     /usr/lib/libz.so.1.2.11
7fbd94a36000-7fbd94b48000 r-xp 00000000 08:13 791982                     /usr/lib/libm-2.25.so
7fbd94b48000-7fbd94d47000 ---p 00112000 08:13 791982                     /usr/lib/libm-2.25.so
7fbd94d47000-7fbd94d48000 r--p 00111000 08:13 791982                     /usr/lib/libm-2.25.so
7fbd94d48000-7fbd94d49000 rw-p 00112000 08:13 791982                     /usr/lib/libm-2.25.so
7fbd94d49000-7fbd94d6c000 r-xp 00000000 08:13 791810                     /usr/lib/ld-2.25.so
7fbd94dcb000-7fbd94f3e000 rw-p 00000000 00:00 0 
7fbd94f6a000-7fbd94f6b000 rw-p 00000000 00:00 0 
7fbd94f6b000-7fbd94f6c000 r--p 00022000 08:13 791810                     /usr/lib/ld-2.25.so
7fbd94f6c000-7fbd94f6d000 rw-p 00023000 08:13 791810                     /usr/lib/ld-2.25.so
7fbd94f6d000-7fbd94f6e000 rw-p 00000000 00:00 0 
7ffdb4d6d000-7ffdb4d8e000 rw-p 00000000 00:00 0                          [stack]
7ffdb4d8f000-7ffdb4d91000 r--p 00000000 00:00 0                          [vvar]
7ffdb4d91000-7ffdb4d93000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
zsh: abort (core dumped)  minialign -l ref_index.mai SubPacbio.fq >| out.sam

Any idea of what’s happening?

About this issue

  • Original URL
  • State: open
  • Created 7 years ago
  • Comments: 22 (12 by maintainers)

Most upvoted comments

Hello,

I have launcher the analysis on a Ubuntu machine and I have no error. It seems to be linked to my Manjaro distribution. But the important point is that I succeeded to use minialign. Thanks a lot for your assistance.