Question: De Novo Assembly Using 'A5' Pipeline
0
gravatar for rwn
4.6 years ago by
rwn400
United Kingdom
rwn400 wrote:

Hello,

I am assembling bacterial genomes (approx. 6Mb in size) using a variety of assemblers / protocols in an attempt to get optimum results. The raw data is 251bp paired-end Illumina MiSeq. There are 2,656,716 reads.

Having given Velvet and Abyss a go, I am trying to get the assembly pipeline A5 (Tritt et al (2012) PLoS ONE doi:10.1371/journal.pone.0042304) to work on my data, but am having some difficulties and was wondering if anyone else has had similar issues (or has got it working fine)...

The A5 pipeline involves numerous stages, but my problem occurs at the assembly stage (A5 uses the IDBA assembler), with the following error message:

[a5_s2] Building contigs from assembly_2.ec.fastq with IDBA
[a5_s2] Building contigs from assembly_2.ec.fastq with IDBA
[a5] idba -r assembly_2.s2/assembly_2.ec.fasta -o assembly_2.s2/assembly_2 --mink 29 --maxk 90
*** glibc detected *** /home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba: free(): invalid next size (fast): 0x000000000239c210 ***
======= Backtrace: =========
/lib/libc.so.6(+0x78bb6)[0x7f6912647bb6]
/lib/libc.so.6(cfree+0x73)[0x7f691264e483]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x40f80d]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45b02d]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45afaa]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45b359]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45b419]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x45ba0b]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x4159c6]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x416b42]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba[0x405d89]
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f69125edc4d]
/home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba(__gxx_personality_v0+0x111)[0x4032d9]
======= Memory map: ========
00400000-0046f000 r-xp 00000000 08:01 29137510                           /home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba
0066f000-00670000 rw-p 0006f000 08:01 29137510                           /home/reuben/bin/ngopt_a5pipeline_linux-x64_20130326/bin/idba
00670000-00870000 rw-p 00000000 00:00 0 
02395000-023b6000 rw-p 00000000 00:00 0                                  [heap]
7f690c000000-7f690c021000 rw-p 00000000 00:00 0 
7f690c021000-7f6910000000 ---p 00000000 00:00 0 
7f6911824000-7f69123c7000 rw-p 00000000 00:00 0 
7f69123c7000-7f69123ce000 r-xp 00000000 08:01 32244320                   /lib/librt-2.11.1.so
7f69123ce000-7f69125cd000 ---p 00007000 08:01 32244320                   /lib/librt-2.11.1.so
7f69125cd000-7f69125ce000 r--p 00006000 08:01 32244320                   /lib/librt-2.11.1.so
7f69125ce000-7f69125cf000 rw-p 00007000 08:01 32244320                   /lib/librt-2.11.1.so
7f69125cf000-7f691274c000 r-xp 00000000 08:01 32244332                   /lib/libc-2.11.1.so
7f691274c000-7f691294b000 ---p 0017d000 08:01 32244332                   /lib/libc-2.11.1.so
7f691294b000-7f691294f000 r--p 0017c000 08:01 32244332                   /lib/libc-2.11.1.so
7f691294f000-7f6912950000 rw-p 00180000 08:01 32244332                   /lib/libc-2.11.1.so
7f6912950000-7f6912955000 rw-p 00000000 00:00 0 
7f6912955000-7f691296d000 r-xp 00000000 08:01 32244326                   /lib/libpthread-2.11.1.so
7f691296d000-7f6912b6c000 ---p 00018000 08:01 32244326                   /lib/libpthread-2.11.1.so
7f6912b6c000-7f6912b6d000 r--p 00017000 08:01 32244326                   /lib/libpthread-2.11.1.so
7f6912b6d000-7f6912b6e000 rw-p 00018000 08:01 32244326                   /lib/libpthread-2.11.1.so
7f6912b6e000-7f6912b72000 rw-p 00000000 00:00 0 
7f6912b72000-7f6912b88000 r-xp 00000000 08:01 32243734                   /lib/libgcc_s.so.1
7f6912b88000-7f6912d87000 ---p 00016000 08:01 32243734                   /lib/libgcc_s.so.1
7f6912d87000-7f6912d88000 r--p 00015000 08:01 32243734                   /lib/libgcc_s.so.1
7f6912d88000-7f6912d89000 rw-p 00016000 08:01 32243734                   /lib/libgcc_s.so.1
7f6912d89000-7f6912d96000 r-xp 00000000 08:01 29622471                   /usr/lib/libgomp.so.1.0.0
7f6912d96000-7f6912f95000 ---p 0000d000 08:01 29622471                   /usr/lib/libgomp.so.1.0.0
7f6912f95000-7f6912f96000 r--p 0000c000 08:01 29622471                   /usr/lib/libgomp.so.1.0.0
7f6912f96000-7f6912f97000 rw-p 0000d000 08:01 29622471                   /usr/lib/libgomp.so.1.0.0
7f6912f97000-7f6913019000 r-xp 00000000 08:01 32244315                   /lib/libm-2.11.1.so
7f6913019000-7f6913218000 ---p 00082000 08:01 32244315                   /lib/libm-2.11.1.so
7f6913218000-7f6913219000 r--p 00081000 08:01 32244315                   /lib/libm-2.11.1.so
7f6913219000-7f691321a000 rw-p 00082000 08:01 32244315                   /lib/libm-2.11.1.so
7f691321a000-7f6913310000 r-xp 00000000 08:01 29628591                   /usr/lib/libstdc++.so.6.0.13
7f6913310000-7f6913510000 ---p 000f6000 08:01 29628591                   /usr/lib/libstdc++.so.6.0.13
7f6913510000-7f6913517000 r--p 000f6000 08:01 29628591                   /usr/lib/libstdc++.so.6.0.13
7f6913517000-7f6913519000 rw-p 000fd000 08:01 29628591                   /usr/lib/libstdc++.so.6.0.13
7f6913519000-7f691352e000 rw-p 00000000 00:00 0 
7f691352e000-7f691354e000 r-xp 00000000 08:01 32244323                   /lib/ld-2.11.1.so
7f6913722000-7f6913728000 rw-p 00000000 00:00 0 
7f691374b000-7f691374d000 rw-p 00000000 00:00 0 
7f691374d000-7f691374e000 r--p 0001f000 08:01 32244323                   /lib/ld-2.11.1.so
7f691374e000-7f691374f000 rw-p 00020000 08:01 32244323                   /lib/ld-2.11.1.so
7f691374f000-7f6913750000 rw-p 00000000 00:00 0 
7fff925ba000-7fff925cf000 rw-p 00000000 00:00 0                          [stack]
7fff925ff000-7fff92600000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted
[a5] Error building contigs with IDBA

I googled the glibc detected: free(): invalid next size (fast) error and understand it is something to do with memory allocation, but this is where I reach the impasse of my understanding. I also read that setting the environment variable MALLOC_CHECK_=1 will not kill the process (I am trying this out now).

But does anyone have any ideas as to why this should be throwing this error? I'm running it on Ubuntu 10.04 (lucid), x86_64 GNU/Linux with 96 Gb RAM.

Any suggestions or experiences would be most welcome!

Thanks, Reuben

illumina miseq • 2.3k views
ADD COMMENTlink written 4.6 years ago by rwn400
1

Look like a bug. You should contact the developers unless you know C/C++ well enough to fix the problem by yourself.

ADD REPLYlink modified 4.6 years ago • written 4.6 years ago by lh330k
2

Yes, I think it is. Actually the problem has been reported at https://code.google.com/p/ngopt/issues/detail?id=6#makechanges already - the issue seems to be the longer read length of MiSeq data...

ADD REPLYlink written 4.6 years ago by rwn400

I am also getting same error ......please help me out

ADD REPLYlink written 4.2 years ago by HG1000
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